I'd say "Captain". I enjoy a bit of accent, but too much gets annoying after a while. And since it's fair to assume Chekov would say "captain" a lot, I'd wager it's one of those instance when readability trumps flair. YMMV, obviously.
I'll also note there is a difference between speaking a language with an accent and speaking a regional variety of that language. Chekov speaks American English with a (supposedly) Russian accents. What I would like to see would be some Russian words and patterns interspersed into his speech: reading "keptin" again and again, on the other hand, gives me nothing of his "Russianity". Scotty, on the other hand, speaks Scottish English, which is a different variety of English. His "wee bairns" are part of his cultural heritage, not a pronunciation defect, and I'm cool with it.