It can be dispelled,which sucks but perfectly reasonable.

But if i want to be a DM worth my salt and prevent the party to just Dispel magic the BBEG i would need something that protects against a no magic zone OR dispel magic... 

How would you do it beyond DM cheese, its nice but overall feels like a cheating positon infront of the players.

Any suggestions?

Just have the BBEG have counterspell when they try Dispell Magic. Or make the BBEGs polymorph an ability instead of a spell.

Quote from Lyxen >>

One good trick against antimagic field (although it's weaker than in AD&D where it was used all the time) is to make it so that the BBEG summoned himself to the prime. That way, he is considered summoned, and he will just wink out of existence if touched by the antimagic field, but reappear when the field disappears.

And then you get into the next trick which is having glyphs of warding that cause part of the ceiling to fall when they are over the center of an antimagic field. Good luck to the caster to succeed on his concentration saving throw when he takes 5d10 of falling ceiling, maybe with save dex for half but no magic items or powers protecting him. And of course the ceiling is high enough that the field does not reach that high... :D

For dispel magic, you can also use glyphs that counterspell it automatically. It's borderline in terms of triggers but it should work.

Also, both of these things are not really unfair as they have a number of charges (the number of glyphs and areas of the ceiling that can fall), and if the players are clever, they  might not succumb to this more than once.

 This is heavy DM cheese, just what the OP seems to wants to avoid. Some spells and abilities are so specific or edge that you almost can't counter them without an intended metagame "cheese". 

Side note, as a player I had to burn a 4th level spell slot a 3 3rd level slots on Dispel Magic just to find out that I was only temporarily subduing an effect...

Quote from MusicScout >>

Or make the BBEGs polymorph an ability instead of a spell.

 This is what I would do. Don't feel that you're constrained by the spells and abilities available to characters. Your creations can do whatever you want, just make the information available at some point so they don't feel directly confounded like wtf's example above. BBEGs are even more special and unique than PCs, and can have abilities that transcend typical spells and their counters.

I tend to use optional, alternate encounter goals to downgrade a BBEG. Maybe if you disrupt the three energy crystals in the room or solve some kind of puzzle, he loses his form - something that makes the fight more interesting than just trading spells and blows.

Maybe the BBEG polymorphed so long ago that everyone thinks that’s his true form. No would would dispel him because no one would think to. 

If your BBEG has access to true polymorph, consider him having a few high CR monsters polymorphed into fragile objects. Each has 1 hp, and takes 1d4 damage when dropped on the ground...

Quote from Xalthu >>

Maybe the BBEG polymorphed so long ago that everyone thinks that’s his true form. No would would dispel him because no one would think to. 

 This. Why would anyone try to dispel something that they don't even know is a spell? That and the fact that dispel magic is not automatically successful is a good start. Making sure that the BBEG knows counterspell also works. And even if they do dispel it, True Polymorph just takes an action to cast so they can always duck down a hallway and cast it again.

Globe of Invulnerability prevents Dispel Magic (and counterspell) on anything inside it, even if you upcast it.

You enemy usually has to:\

1. Dispel Magic on the Globe. 
2. So you Counterspell that Dispell Magic
3. They can NOT counterspell your counterspell, as you are in a Globe.

Players casting dispel magic to un-polymorph your BBEG is only a problem for you if you want it to be.

Also, here is another trick with True Polymoprh.

Fill a large fragile non magical glass object container with a lot of a dangerous non-magical substance - poison gas, acid, poison, disease, whatever.

True Polymorph it into a big creature, which becomes friendly to you.  Send it into attack.  Once it is killed, any extra hitpoints spills over into the large, fragile, glass object.   It breaks, releasing the nasty death.

Extra special treat for the bad guys.

Quote from Mog_Dracov >>

Also, here is another trick with True Polymoprh.

Fill a large fragile non magical glass object container with a lot of a dangerous non-magical substance - poison gas, acid, poison, disease, whatever.

True Polymorph it into a big creature, which becomes friendly to you.  Send it into attack.  Once it is killed, any extra hitpoints spills over into the large, fragile, glass object.   It breaks, releasing the nasty death.

Extra special treat for the bad guys.

 Thats an amzing idea overall, thank you!