Well, I have no idea how on earth you would choose - the Bee and the Nuna are my 2 complete favourite buggies.. of all time!
Before I start, could you not just buy second hand of both, and have 2 buggies?
The Nuna and the Bee push very similarly - turn on a sixpence, and are very very smooth; you can easily push both with just one hand, or even your little finger.
The fold of the Nuna is just brilliant, could fit in a footwell if necessary, and it pops back up so easily too. I do have to say though, there is a slight issue with kerbs.. this is just a random image, but will help explain what I mean - here .The underneath bit is really low down, and so when you go down a kerb it often scrapes that bit. Have had a few times where it's been a high kerb, and have rushed to go down it, the buggy has then got stuck mid-kerb-flight; when you then go to push it with your foot, you put the brake on and you're even more stuck. It only happens very rarely, and on big kerbs, but it could be a slight issue. The harness is a nightmare, but I've always wondered whether you could just superglue the bits together so that you've just got a plain 2-point harness? The seat is brilliant - especially around the age of your DS; it puts them in a great position for sitting up, and supports them really, really well. It is quite a narrow seat, but I see this as an advantage as it kind of keeps them in place rather than having DC's lolling around in there and slumping to the side?
Onto the Bee, which has always been an all time favourite. It really does do everything, and whilst I can come up with a few 'niggles' about the Nuna, I can't really think of many for the Bee. Obviously it is more expensive, but I do think that with Bugaboo, you pay for what you get - they're brilliant and last forever. The seat can occasionally be a bit difficult when you first get it - takes a bit of getting used to with putting it backwards and forwards.
It is really tricky, but I think, despite my total love for the Nuna, I'd go for the Bee. It's more of an 'all-rounder' I suppose?
Definitely go into JL and try your DS in them and push them around though - is the only way that you'll get a good feel for them both, good luck! :)