I am currently lvl 1 and have taken one handed and small frame with high agility, perception, luck and intelligence for my character. I use these 3 skills Small guns, Steal, lock pick and minor in science and repair. I usually just blow up the base but this time I want to be able to fight the bastard with powerful pistol in hand. I don't want to use rifles as I want to use a pistol for one handed.

Is this possible or should I just blow him up? I watched a video on youtube where some guy took him on but he was using a rifle. Melee isn't possible so I just want to know. Thank you.

Yes, it's possible. But I advice you to bring some npcs with you, to distract the super mutants.
And a tip, this will make the battle easier: if you can, hide in the pillars before ending your turn. The master can't hurt you. :)
Don't forget to get the .223 pistol.

Edit: since your Steal skill is high, you can get a lot of stimpacks easily. Search the guards' pockets in The Hub. ^^

Totally possible and the .223 pistol is a great weapon and the best weapon, as far as pistols go, in Fallout. The master isn't really that hard, except for those pesky criticals he gets sometimes.

Also keep in mind there will be mutants spawning in the corridor to the master, who give me a lot more trouble than the mutated overseer chair and its turrets.

As almabrds mentioned a follower or two don't hurt and if you get him to shoot the robots they also will attack him and distract him for one or two turns, giving you just enough time to use that crucial stimpak. If you don't mind the hassle, that is.

*edit*

Hah! Nevermind. almabrds already said it. The weapon doesn't matter--the master can't hurt you if you use the pillars.

HINT:

Have you ever tried convincing him he's wrong?

He does inflict some stat penalties on you before you get up close to him, but those can be mitigated.