A good alternative to Ensenada Honda is Bahia de Sardinas, which is at the SW end of the Laguna de Lobina, off the ferry dock. It’s quieter, it’s more scenic, has great holding, and still offers a short dingy ride to town. If you’re coming from Vieques, it’s also a shorter trip.
I think Nibj is referring to the other, not be confused, Ensenada Honda towards the eastern end of Vieques. We anchored there - it was fine. Great protection and very calm, but water is a bit murky. You can explore the mangroves by dinghy, but we had rain so we skipped it.
As for #2, we skipped the Mosquito Bay bio tour also because of rain. We opted instead to anchor at Puerto Ferro - didn't see anything. It's another murky, mangrove lined bay with a few abandoned sailboats. There are nicer places to spend a night.
I too prefer Culebra and probably won't be back to Vieques soon. For your trip consider adding in a lunch/snorkel stop at Bahia de la Chiva. We also really enjoyed Punta Arena on the west end. Scenic spot, good snorkeling, and great sunsets over the Puerto Rico mainland.
