AK
HI
USVI
PR
GUAM
U.S. Citizens and Lawful Permanent Residents (LPR's) who travel directly between parts of the United States, which includes Guam, Puerto Rico, U.S. Virgin Islands, American Samoa, Swains Island and the Commonwealth of the Northern Mariana Islands (CNMI), without touching at a foreign port or place, are not required to present a valid U.S. Passport or U.S. Green Card.
https://help.cbp.gov/app/answers/detail/a_id/980/~/needing-a-passport-to-enter-the-united-states-from-u.s.-territories
You went on a cruise ship. Different situation.
Last time I checked, yes, although way back when I was in Dago, it wasn't a requirement to cross into TJ.