I was booked one night at the Mariott Waterfront and one night at the Mariott Inner Harbor late last month, but moved both nights to the Inner Harbor for the in-room internet (both booked with that great travelzoo offer).
The Inner Harbor hotel was quite nice. Easy walking distance to the Aquarium (absolutely gorgeous March weekend), the water taxi to Fells Point and Fort McHenry, and everything else. I did room service for breakfast and dinner and enjoyed both.
I also hit John Stevens, Ltd. for lunch at Fells Point on the advice of my water taxi Captain and it was as good as he said it would be (had the crab cakes and fried crab ravioli).
So for stays in Baltimore itself, it's the Inner Harbor property for me!