Black Mask is a very simple boss. There are 3 different stages of this boss fight.
I've attached a video that will show everything, and is only really needed for the Stage 2 section. The actual fight starts at ~21:00 in the video
Stage 1You will need to fight off a bunch of thugs as Black Mask throws grenades down at you. Very simple and straight forward.
Stage 2This is the most complicated stage of this boss fight. It consists of using your explosive gel on 3 buttons and setting them off at the same time to override the generators and follow Black Mask through the door. You will fight 2 groups of thugs at different spots, but other than that, this section is devoid of enemies. Follow the video and you will get through this without an issue.
Stage 3This stage pretty much sums up Black Mask as the lamest boss ever lol.
Using your analyzer

, analyze the far left light and the alarm ( I didn't have to analyze the alarm, it was already yellow). Select your Batarang with

. Hold

and select your target with the left stick, aim for the far right alarm and use

to hit it. BM will shoot right, quickly hit the light with your Batarang as well, then quickly jump into the grate using

+

.
Once he finishes shooting move to the far right grate and get out, then target the far left alarm and hit it with your Batarang. Jump back down into the grate and move left, if you are quick enough you can get him while he is walking left. Use

to perform the take down and end the fight!
If he walks to far for you to get the take down, he will simply stand still and not move. If this happens jump out of the far left grate, hit the right alarm, then jump back down the grate then perform the take down as he is walking right.
Credit for the video goes to youtube user: Batman Arkham Videos