There are many per the list linked by @Valorum.
But the following are quite unambiguous:
- USS Albert Einstein
- USS Crazy Horse
- USS Elmer Fudd
- USS Farouk El-Baz
- USS James Fennimore Cooper
- USS John F. Kennedy
- USS John Muir
- USS Max Plank [sic s/b Planck]
- USS Neil Armstrong
- USS Neils Bohr
- USS Robert Louis Stevenson
- USS Sherlock Holmes
- USS Thomas Paine
- USS Yuri Gagarin
This is not even including those that are almost certainly supposed to be named after male mythological entities:
E.g. Apollo, Hermes, Prometheus, Ulysses
And not including those that are almost certainly supposed to be named after notable historical surnames that are almost certainly supposed to be based on specific male historical figures:
E.g. Archer, Armstrong, Bradbury, Chekov, Cochrane, Cooper, Copernicus, Cortez, Crockett, Drake, Edison, Farragut, Fleming, Glenn, Gorkon, Grissom, Hood, Hoover, Horatio, Kelvin, Korolev, Livingston, Magellan, Nash, Pasteur, Potemkin, Profokiev, Roosevelt, Rutledge, Sarek, Shepard, Shran, Suleiman, Tolstoy, Truman, Tsiolkovsky, Tycho, Wellington, Yamaguchi, Yeager.
Here I've bolded certain names that, because their association with astronomy, discovery, aeronautics, or their origin in the Star Trek universe, I consider to be obviously based on the obvious well-known male figure.
(I mean, come on. We don't know there wasn't a 22nd century Andorian woman named Elmer Fudd either so I don't see why we should consider a full name to be any more conclusive than Shran, Sarek, or Yeager)