It's a very interesting question. In terms of which game I'd rather play, it's SMW. But in terms of technical achievement, SMB3 is unquestionably better (in my opinion of course).

SMB1 was a watershed moment for gaming - perhaps the biggest that there ever was. SMB3 was a revolutionary improvement on top of that. In light of that, SMW almost feels like a bland port. This isn't to say it's bad by any means, but in terms of the impact that it had on gaming as a whole, it's not very significant and just feels like an iterative improvement.

SMW is still a great game! And if I could only play one for the rest of my life, I would choose it over SMB3. But in terms of historical impact on gaming, I would say that SMB1, Mario64 and SMB3 were more revolutionary.

Yoshi's Island is my favorite however.