In Winter Soldier, the antagonist is a man called Alexander Pierce.
In Logan there’s a bad guy called Donald Pierce.
In the comics, are these two related?
No. At least not yet. The MCU just lifted the names of characters tangentially related to the movies.
Alexander Goodwin Pierce was/is a SHIELD agent in the comics, had a couple of supporting roles.
Donald Pierce was a member of the Hellfire Club, X-enemies from way back. He’s a cyborg like in the movies and, IIRC, the creator of the Reavers, a group of cyborg mercenaries. They are unnamed in the movie. Lady Deathstrike is also affiliated with the Reavers, she showed up in X2.
Truer words were never spoken. Sooner or later, some writer/editor will realize that we have two guys named Pierce, and they will become familially connected. (yes, I think I just made that word up) It’s a 99% surety, just a question of when.
The White King, in the Hellfire Club, before he took off to the Australian outback with the Reavers.
Jefferson Pierce is unrelated to either, too. 
Are we certain? Mr. Sinister was around during the American Revolution, a quick trip over to Monticello with his test tubes and a lightning rod. 