Scott did not have many friends growing up, but he did have one in particular: Leonard McCoy.
They met when they were kids, when David McCoy brought Leonard to Aberdeen. It was only three times, but it was enough just to say that Monty had more than one friend who wasn’t his brother, Robbie.
However, when Leonard’s aviophobia kicked in, he never really saw him again–and it was rare for that, as they were attending the same Starfleet academy together. They saw each other once or twice, but that was it.
So, Monty remained friendless. It was easier, because he knew no-one wanted to befriend the Scotsman with an Intelligence Quota of over 128. Devoted himself to his studies and even Scotch. Anything to distract himself that he spent the majority of his life alone. And it carried on that way, including Delta Vega.
Yes Keenser was there, but he wouldn’t hear from him for days, sometimes weeks. When Jim Kirk and Prime Spock showed up, it was one of the few times within that particular month that Keenser spoke to him. Yes, they were partners–didn’t mean he wasn’t not lonely. He did like the occasional conversation, the knowledge that he wasn’t boring someone to the point of death. And even though Keenser couldn’t utter more than a few words, it was fine. Of course, it would be fine. Wouldn’t bother him.
But it did. It bothered him so much.
After the fight scene on the bridge, Montgomery recognized that doctor–noticing that it was the kid from Georgia and now he was on board a ship with him and it was McCoy who helped Scott get a towel to dry off. Because Scott wanted it to be him, so they could catch up on the minor things and so that he could understand what just happened.
And, maybe yeah–working in a crew that could substitute as your family is nice, but he can go without days without seeing the bridge, without speaking a word to Sulu, Chekov, Uhura or Carol Marcus. The only real friends he talks to on a regular basis are McCoy and Kirk. Although, the latter is mainly required–because he does work as the Engineer and Kirk needs to know what is going on with his ship.
But his friendship with McCoy is different. There’s a mutual understanding of each other, that they’re on-board, sometimes so lonely and self-destructive. They drink often with each other, commenting on Kirk’s brilliant ideas with frequent sarcasm. That Monty sometimes needs the reassurance that there is someone in the universe who wants to talk to him–not for his transwarp beaming equation and not for the ship; but for company.
So that would explain why Montgomery Scott would call Leonard McCoy his best friend and not Keenser. Because he found someone who wants to spend time with him, who is not complied to.