Like Stu says, Montague, Pender, etc... all great. Last I heard, the marina/dock at Fulford was wiped out last winter. Maybe it's back, but check. Are you taking kids with you? Ganges is nice. North Pender (Port Browning) is quieter and has more space, but the marina is not that great. But it is only a short walk to the market, good bakery, and nice restaurant. Bedwell has a realyl nice marina and a resort with a great pool.
If you're up for dropping over the border and hitting the San Juans, Stewart Island is super (be sure to walk to lighthouse), and Garrison Bay and Wescott Bay near Roche Harbor are nice (but can be crowded in summer). Roche Harbor is really nice with huge boats and all, but you can also take the bus and explore the island from there.
Also, if you are going to cross the border, it might be quicker just to head to the south end of San Juan or even to Lopez. I like Lopez a lot. Feel free to email if you have questions.