The Mk4 is a heavier car, and if you only get the 150bhp version it's got less bhp per ton than a Mk3 16v (which is also 150bhp).
So the Mk3 VR6 is older, and it's only a little lighter than the Mk4, but it's got more power to begin with.
The Mk3 isn't that old anyway, I saw an S reg recently, so that's a 98/99 car.
As someone said it's down to wallet and preference really.
A good Mk3 VR6 will be £3-4k (for decent milage, you can get them for less if you'll accept higher milage)
An early Mk4 1.8T will probably be about £5k
Later Mk4 1.8T upto £8-9k
As for the Mk4 TDI's, they're getting very popular especially with the chipping possibilties.
You can find them for as little as £3-4k for a 130 or about £6k for a 150.
Best to check out your favourites to see which you prefer to drive.