Shadow Dancer

Getting Lobster Commander from bases can be tricky. Try getting one in your backpack before ending the mission, it might work. But the best way by far is from Dreadnaughts with lobsters. You'll need at least one Manta armed with 2xSonic Oscilators, and there's a chance your fighter will be destroyed in the firefight, so save the game before the intercept. Once you take down the Dreadnaught, kill every lobster you find except the ones on the top level, one of them is the Commander, use either a MC reader of MC distruptor to make sure which one is, usually he is unarmed visually but so are the Navigators.

About the topic, Sonic Cannons or Rifles... it's simple. Know your enemy, if they are Tasoth/Lobster/Brain, you need Cannons because it kills in 1/2/1 hits usually and at full APs you can get 2 deadly accurate snap-shots. Other enemies can be killed in one hit with Rifle so it's better in this case. But in any case, keep a few MC soldiers to make sure the enemy has no chance of retaliating. Now which weapons are the most effective vs Lobsters... it's simple. MC Distruptor and Vibro-blades. Snipers with Sonic Cannons are also quite powerful against them.