Avoid American hotels in Prague at any cost !!!!!!
I really recommend the Hoffmeister. It's a Relais et Chateaux hotel. Don't be put off by the location near a main street.
The Savoy is also a good one, although up to a some time ago it was owned by Lybian interests and US residents were not allowed to stay here (in theory at least...). Even if you do not stay at the Savoy, try the breakfast there, it's the best in town even if a bit pricy on Czech standards. I love the location of the Savoy, a little out of the way but still close enough to the castle, and the tram stops right in front.

If you held a gun to my head- and it'd HAVE to be a real big one, and I only had a choice between the 3 you mentioned, I'd stay at the Marriot. If you like this sort of thing, it's brand new and you can't beat the location near the gorgeous municipal house ( check out the restaurant in the basement, art nouveau heaven).
and one thing: watch for taxicabs who will rip you off from the airport. Negociate the price in advance, not more that 600 crowns to go downtown.
Have a great time, say hi to Vaclav and go check out the Last Judgment Mosaic on the cathedral.