We recently spent 5 days camping on Assateague Island in Maryland. We stayed in the National Park Service campground and were on the bay side. Our campsite opened right onto the bay. We were able to launch right there. It was more convenient than I would have expected.
We only did day trips. They have longer trips and camping available but that wasn't what we were interested in. www.nps.gov/asis provides information about the possibilities and restrictions. The bay is shallow. Enough so that you shouldn't have much trouble with bigger boats with motors. At low tide, it can be a struggle to get to water deep enough to easily paddle. High tide was better but still kind of shallow.
We were able to get close to 5 ponies grazing along the water. We enjoyed them. It was getting ready to blow up a storm so we couldn't hang around as long as we wanted to. If you like ponies and shore birds, this is an excellent place to paddle. They have problems with mosquitos in the summer but not in April.
Ocean City and Berlin both have the usual assortment of hotels. We camped at the Bayside campground which NPS runs. They have mostly large sites. Around 10 have water access. Facilities include chemical toilets and cold water (nearly outdoor) showers. You can walk to the ocean from the bay side sites.
$5 for a 7 day permit for the park. I think camping was $16 per night.
Take Rt. 50 to Berlin or Ocean City, MD. The routes to Assateague Island are well marked.