My two cents, though I've never GMed Shadowrun (just D&D)--here are some ideas for scaling the difficulty of the mission to the smaller group size:
= Bump up to 500 BP could probably work, but it might work better to do 400 BP and then give them an appropriate amount of karma (so they can treat this as a character that has run a few missions, but is otherwise new). Grain of salt; like I said, I'm new to the system.
= Make it a little easier. Require a lower threshold on some tests, and either reduce the number of goons they have to fight, or make them a little weaker.
= Let a player run two characters (not a good idea if they're new to the game or to tabletop RPGs in general, but I've had it work out before)
= Just an idea, but maybe give them a "freebie" point of Edge--use only (not to be replaced whenever they would earn an edge point, but just to give them an edge (pun intended) on the mission. After all,
everyone loves the underdog!
Again, my advice is based on experience playing and DMing D&D, but I feel I should point out that 3-5 players is usually the target number for me, because it's enough variety that I can throw all kinds of challenges at them