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Sorry that no one has responded to your post yet. In case you haven't made your choice yet I hope this helps.
 
School A seems like a better choice in terms of fit and the status of the program. I'm going to a relative new program but two-years-old seems a little too new to me; it doesn't sound like you are interested in clinical but on the chance you are a two-year-old program may not be accredited. And while connections with others are important, I imagine there'd be more opportunity to do that where ever you end up.
 
For me, knowing how I would pay the bills and put gas in the car is just as important though. Certain parts of New England can have a ridiculous cost of living, and then there's the difference between rural and RURAL New England. With gas prices as they are, I wouldn't want to isolate myself too much on my stipend, even at $24k.

Personally, I would believe the grad students (especially multiple ones) over what the PI claims wrt amount of time spent and accessibility.  Academics tend to be people who enjoy spreading themselves thin and often don't realize when they are spread too thin.  This may not be as much of a concern for you, though, if you are a more independent student.  My advisor is very busy; although he can always make time to meet with me if I request it, I request it less often because I prefer to be left alone to work as I see fit.  My PI also does not have tenure, but I like that because it makes him "hungry" and we have done a lot of good work together.
 
Are you interested in conducting research abroad?  This isn't that common across psychology (certainly not in my subfield), so that would be less relevant unless your research has significant international connections or implications. If you're using experimental or computational methods I don't see why you would be doing significant research abroad.  Greater resources, though, may translate into more travel funds to go to conferences and things like stats packages, computers, that kind of thing.
 
Also, a new program can be a con as well as a pro.  More established programs don't necessarily mean more complacent faculty; they can mean faculty who have really invested in the success of the program and the program already has a proven track record of success.  Newer programs are less tested and may be riding on the success of a few people there; if they leave, the program may tank.  (Unlikely, but possible.)
 
Research is king, so I would be leaning towards School B - more resources, a wider range of methodologies, and an admitted chance to do more research.  However, you do have to consider the shortcomings.  Classes can be misleading; there may be fewer classes on theory and computational methods, but can you *learn* those things there other ways?  There aren't many classes in my department at all but I've learned so much here through working with people and teaching myself things with mentorship.  Really, that's the way academics learn after a certain point.  Can School B make up for that weakness through mentorship and seminars?  Also remember that if they have better resources, they may be able to pay for you to take summer classes or attend a summer institute at APA or Michigan's ICPSR or a similar program to learn those methodologies.  Ask about that.
 
Student happiness is important, but you only interacted with 2 students.  Is that two out of 3 TOTAL students (because that's a problem, then!) or just 2 out of the 3 students you interacted with?  And why are they unhappy?  That's important.  If they are frustrated with the way their PI treats them and the lack of opportunities in the program, that's bad.  If they're unhappy because the location is remote and they want to date, or because they've had interpersonal problems in the department, then their experience may be less relevant.
 
However, my comments are only based on the information that School B would allow you the chance to do more research.  If you reassess and don't think that's actually true, then I think School A may be the slightly stronger winner here.

I second what everyone suggested. And you should take advantage of the interview for a few additional reasons: 
 
1) Preparation. The more interviews you attend, the more comfortable you'll feel speaking with professors, and the better prepared you'll be for the next one. This is especially true for me since I don't interview well to begin with.
2) Networking. You might end up collaborating with these professors one day, or you might end up applying for a post-doc or faculty position. I think it's worthwhile to start forming these relationships. If anything, it puts you on their radar.
3) Complete experience. You get to see what graduate life is like, both in and outside of the lab. You might be pleasantly surprised (or maybe disappointed) with what JHU and the surrounding community has to offer.
 
I also sent you a PM.

I second what everyone suggested. And you should take advantage of the interview for a few additional reasons: 
 
1) Preparation. The more interviews you attend, the more comfortable you'll feel speaking with professors, and the better prepared you'll be for the next one. This is especially true for me since I don't interview well to begin with.
2) Networking. You might end up collaborating with these professors one day, or you might end up applying for a post-doc or faculty position. I think it's worthwhile to start forming these relationships. If anything, it puts you on their radar.
3) Complete experience. You get to see what graduate life is like, both in and outside of the lab. You might be pleasantly surprised (or maybe disappointed) with what JHU and the surrounding community has to offer.
 
I also sent you a PM.

Welcome to GradCafe!
 
I'm a Fall 2013 applicant, so I have never had a conversation with a POI by phone or by Skype. However, I have used both for job interviews. 
 
The advantages of the phone include not stressing what you are wearing (although, dressing up can mentally make you feel prepped!). However, the conversation can be awkward, such as when there are pauses during the conversation and you and your POI speak at the same time.
 
The benefits of Skype are seeing each other, where you both will be able to tell visually when to speak and when to listen. Also, you will also have the chance on Skype to pick up on non-verbal cues from your POI, which can indicate interest, e.g. nodding, smiling.
 
If you decide to go forward with Skype, I recommend trying it out someone else first, to see how it works, and to practice responding to the questions looking into the webcam (rather than looking at the interviewer or down). You'll look on the screen like you are looking straight ahead at the other person. Also, fiddle around and place your computer so that the background behind you is appropriate for the conversation.
 
Good luck!
 
 

I agree with ArtHistoryandMuseum - the phone can be awkward! I've had conversations with POIs both over the phone and with Skype and I prefer Skype. The best things about Skype are that you can see when the POI is taking notes (which makes it much easier to know when to pause) and what his/her reaction is to what you've said. Also, my kitty came to visit during our Skype chat and it gave us something to joke about and eased the tension. 
 
Good luck with your interview, whichever you choose!