I just completed the MA in Media Studies at The New School entirely online, and I'm in the process of applying to Ph.D. programs. I'll let you know if they snub me!
I've had many in-person chats and email exchanges with professors and students at several of the top programs. The online aspect only came up once in conversation, and I didn't get any sense that it was considered a knock against me.
If you do get into one of these programs, try to make yourself present as much as possible at the school and/or at conferences and other events. Doing a program online doesn't mean you have to be uninvolved.
Also, it's very possible to develop strong relationships with professors in online classes. Participate as much as possible, do all the assignments to the best of your ability and tackle something of substance for your thesis.
There may be a stigma to online programs, but I think more weight is given to a school's reputation and what you have to show at the conclusion of your program. And doing these programs online is not as easy as some people might think. Sure, you COULD slack off and phone it in. But you can do that on campus, too. These programs are really what you make of them.
Good luck!