Definitely check the New Media program list with Rhizome first. I'm in the MFA program at RISD right now and can say that it offers a lot of flexibility and resources to students. As a note, we're in the middle of an international search for a new department head which should end at the end of this academic year. Feel free to email me if you have any extra questions. The programs website is here: http://dm.risd.edu
You can also cruise this mega list of national new media programs:http://www.iupui.edu/~j21099/nmschools.html
It's not exclusively MFA but it's a good starting point for broader research on schools.
I know SVA just started an Interdisciplinary MFA program that might be worth checking out:http://www.aphotostudent.com/2010/07/26/sva-announces-new-mfa-program-led-by-david-ross/
I've had a few friends who have gone to ITP too that had a good experience. The RISD program is geared more toward Fine Art and you can take courses at Brown - ITP is more technically focused. At least that's my understanding.