I've only tried a few of the many restaurants in teh Inner Harbor, but there are lots of them:
Capitol City Brewing Co, in the light Street pavilion of Harborplace, had great food at reasonable prices.
J Pauls, also in the Light Street pavilion, is also terrific.
Phillips is top-knotch, though a little pricey.
On the east side of the harbor, the Hard Rock Cafe is very good, though a little noisy.
Way over on the west side, past Rash Field, is the Rusty Scupper. I haven't eaten there myself, but it has a great reputation around here. It's a bit pricey, though.
Another I have not tried is Windows, on level 5 of the Rennaisance Harborplace Hotel. Also gets great buzz around here, and also a bit pricey.
There's also a very cool place on the top floor of the Hyatt Regency Hotel called Bistro 300, supposedly some of the best seafood in town. It has the best view of the city and is moderately pricey.
Be sure to leave room in your schedule to try some of the counter-service places for lunch. There are a few little sandwich shops and delis in Harborplace that have terrific food at good prices. And there are also the Cheescake Factory and two ice cream places for dessert, and a fantastic candy place on the lower level of one of the pavilions that puts on a show of mixing chocolate a couple of times a day.