There are many places inside Seal Bay and Winter Harbor to anchor.
One of the “snuggest” and most secluded is all the way up in the inner harbor of Seal Bay, as far past Burnt Island as your keel will allow. The charted depths are remarkably accurate, but take care given the tidal range. One rock you’ll need to avoid is between Hay (smaller) and Penobscot (bigger) islands. Favor the Hay Island side of the channel, go slowly, and you’ll be fine.
Another popular spot for those who’ve been to Seal Bay a few times is the cove to the SE of Hen Island just after turning the corner to enter Seal Bay. There is deep water (35 feet or more), and as long as the wind doesn’t pipe up out of the north, it will be very comfortable. Also, if you’re feeling brave (and careful), you can sneak out the narrow channel to the north. Everyone will wonder where you went.
There are several anchorages going farther into Winter Harbor. One of the best is in the deepwater “hole” opposite Starboard Rock — being careful to avoid the two-foot spot noted on the chart. Depending on your boat’s depth (and your adventuresomeness), one can anchor farther up this harbor, but the channel is littered with rocks and has shallow edges.