Assuming you can count Stan Lee out, since he makes a cameo in almost every Marvel movie, then without a doubt it's Chris Evans.

He has played 4 roles derived from comic books:

• Johnny Storm in Fantastic Four (2005) - Based on the Marvel Comics book

• Jake Jensen in The Losers (2010) - Based on the Vertigo comic book

• Lucas lee in Scott Pilgrim vs The World (2010) - Based on the graphic novel Scott Pilgrim

• Steve Rogers in Captain America (2011) - Based on the Marvel Comics book

and (for the sake of completeness) 1 role in a movie which spawned a comic book:

• Nick Grant in Push (2009) - Spawned the Wildstorm mini series

Lou Ferrigno has five…

…if we count different incarnations of the same character as "unique".

Hulk — Films related to The Incredible Hulk TV series

• The Incredible Hulk (1977 pilot film)
• The Incredible Hulk Returns (1988 made for TV film)
• The Trial of the Incredible Hulk (1989 made for TV film)
• The Death of the Incredible Hulk (1990 made for TV film)

Security Guard — Hulk (2003)

Hulk (voice) — Hulk (2003)

Note that this film is not in continuity with either the TV series or the Marvel Cinematic Universe, thus this is a different Hulk than than those ones.

Security Guard — The Incredible Hulk (2008)

While this is the second time Lou Ferrigno has played a security guard in a Marvel movie, the two films are in different continuities and are not implied to be related.

Hulk (voice) — Marvel Cinematic Universe films

• The Incredible Hulk (2008)
• The Avengers (2012)
• Avengers: Age of Ultron (2015)
• Thor: Ragnarok (2017)

Wikipedia notes that Ferrigno was credited for The Incredible Hulk, but had uncredited "voice collaborations" for the remaining films.

Donal Logue:

• Gotham (DC, TV) - Harvey Bullock
• Ghost Rider (Marvel, movie) - Mack
• Blade (Marvel, movie) - Quinn

Also, when it comes to TV & Movies, both live action and animated, there are many actors that play multiple characters and voices. Here are two that come to mind that have played MANY roles and voices.

• Micheal Rosenbaum
• Clancy Brown - Just glancing at his IMDB page, he has over 30 roles in Marvel and DC movies, TV shows, and games.

Stan Lee, he plays a different character in every Marvel movie. Another thread already has a fairly updated list going https://scifi.stackexchange.com/questions/37092/actor-with-the-most-comic-book-movie-roles

Depending on whether his role as Commissioner Gordon is up to scratch on Justice League and The Batman, J.K Simmons would have played J Jonah Jameson, a chaotic Marvel character and Jim Gordon, a more calm character.

Besides @johnny's answer I would like to add (as a honorable mention) actor Josh Brolin who played/currently playing 3 comic book characters from both DC and Marvel:

• DC's Jonah Hex in the movie Jonah Hex (2010).
• Marvel's Thanos in Guardians of the Galaxy (2014), Avengers: Age of Ultron (2015) and the two upcoming Avengers: Infinity War (2018) and Untitled Avengers film (2019).
• Marvel's Nathan Summers / Cable in the upcoming Deadpool 2 (2018) which is in post-production (shooting is complete).

Note: The reason I added Josh Brolin, even though he is beaten by some other actors in the other answers, is because of the importance of his characters and the size of his roles in the aforementioned movies.

Like Chris Evans, Ryan Reynolds is now a veteran with many roles under his belt:

1. Hannibal King in Blade: Trinity
2. Green Lantern in Green Lantern
3. Deadpool in Deadpool 1 & 2
4. Nick Cruz in RIPD

Arguably, the character he played in X-Men Origins: Wolverine is a different one from Deadpool as

Deadpool shoots him in the end credits of Deadpool 2

I'd say Alfre Woodard, who played two very different characters in the MCU alone:

Miriam Spencer, a grieving mother in "Captain America: Civil War"

and

Mariah Dillard, a shady Harlem councilwoman and a villain in Netflix series "Luke Cage", seen here with her gangster brother 'Cottonmouth'