The only advantage I can see to the Ancestry visa is that it gives you 5 years in the UK and you can then look for another job here after your post-doc runs out (and they are easier to extend further); your Work Permit visa would probably be limited to the 2 or 3 years of your post-doc. This kind of visa can be extended, but only by the same employer--so it's harder to move around.
So which you go for may depend on what you want to do next, but you might also consider the hassle-reduction of having your institution help you. I've not heard of anyone being turned down yet, but the process does take longer than it did.
The other advantage is that the UK university is likely to pay the full fees for a work permit, but may be reluctant to pay for an ancestry visa.