IMO, the HoJo is the nicest of those on that strip of Harbor closest to DLR. The HoJo is a true hotel (indoor corridors to rooms) not a motel. It has two pools, a hot-tub, and a kids pool. The property is older, but the rooms have been renovated (I believe they are now completely done) and the property and rooms are extremely well maintained and clean. The rooms are reasonably large, especially the home office rooms (my recommendation). If you are traveling with kids then HoJo would definitely be my #1 choice.
Next on my list would be the Candy Cane (not on Harbor, but just as close). They have nicer toiletries and a complimentary breakfast. They try very hard to be more of a boutique motel. The pool is small and the rooms are smallish too. If it's just adults and the pool isn't an issue, then Candy Cane is the best bet.
Many of the motels nearest the crosswalk on Harbor are older, 2 star kind of places. Tripadvisor has reviews for all the hotels in the DLR area, defintely check them out.