I think long distance is easier to manage than most people think. I mean, its impossible to not communicate. We got cell phones, instant messaging, and WEBCAM (My favorite! ). The only real thing you miss is the 'physicalness'. I think the hardest thing to manage is to dedicate time each day to be able to sit down and TALK. And no, I don't mean sit down and talk WHILE WATCHING TV OR SURFING THE WEB. I mean sit down and talk,talk. Give 110% nothing less! Of course, I also make an effort to try to visit her once every 1-2 months. And of course, I'm with her over summer.
Now, in my opinion, since your both PhD's your going to be so busy you wont have much time to really miss each other. You'll both be wrapped up in research even if you were going to the same school how often would you actually be able to see each other?
IMHO I would pick the top school, you got the rest of your post-grad life to spend with him!
Good luck
