So basically my courier is a bit of a renegade, scorned by life many times. He is going to side with Yes Man for the battle of hoover dam but I kind of want to shape the ending in a certain way.

I want to obliterate the NCR and the Legion. Their leaders as well.

Then, I want to wipe out the Brotherhood of Steel, Omeratas, Ultra Luxe folks, The Tops, Great khans & leave the Boomers alone.

Is it possible to have this outcome where all said factions get wiped out and New Vegas can prosper from independance without the concern of any remnants of the other major factions except the boomers as allies?

Check out Yes Man's missions where you investigate on the various factions. There's usually an optional objective that tells you to kill the leaders and such.

AFAIK it's the only way to ''obliterate'' them.

Sure but don't go to the dam to deal with NCR and Legion until last.

Takeout the Brotherhood of Steel, Omeratas, Ultra Luxe folks, The Tops, Great khans first.

I assume you have already cleared vault3 and the surounding area.

Ok thanks, and no I haven't cleared out Vault 3? Omeratas & Ultra Luxe down, getting there

Wiping out Vault 3 and the Fiends will help your character. Call it an unmarked reason to help bring the area under control.

Ah ok that's useful. Also I did the white gloves / ultra luxe quest. I save Ted and returned him to his father. Afterwards I killed every white glove inside the hotel, but I'm not vilified for some reason? I'm "wild child" despite being vilified and then somehow my rep got better after I killed all of them?

The option for yes man is now "Inform yes man you fixed their canabalism problem". This would still count as destroying them right?