I'd like to take a trip to Baltimore for a few days. Are there any inexpensive motels/hotels near the harbor?

There are hotels by the harbor (no motels). And they are all expensive. Expect to pay at least $200 a night.

2 good alternatives would be Fells Point, where you could take a water taxi to the harbor or by BWI where you could take the light rail. And go on weekends. Baltimore is primarily a business and convention city, so weekends are less expensive.