I noticed that there are side quests you can get along with the main quest (the Goodsprings vs Powder Gangers for one). Just wondering, these will be available at any point in the game, right? That is, except when I actually finish the main quest, because then the game ends.

Yep, should always be available, unless there is some quest later that deals with the same thing. Haven't run into that problem yet however (just beat it) so you should be fine.