I like them both but in vacuum, chip vs chip, I think I like the 43s a bit better, because there's "more of it" in each chip, LOL!!!.
Having said that, in terms of playability, things get a bit more complicated for me. For cash sets, where stacks can get huge, I favor 39s. For tourneys, I think it's a push between 39s and 43s as chips get color up and stacks tend not to be huge (unless one uses antes, in which case, I'm back on the 39s train).
I'm not a huge fan of mixing sizes if those chips are workhorse chips. It's not optimal for me to get a few 39 $5s and a few 43 $25s to make a bet. I'd prefer all 39s. Now, a "value" chip being oversized I don't have a problem with, chips that don't get bet with too often.
So in summary for me:
Cash Sets: all 39s > all 39s with 43s high value chip > all 43s > 39s and 43s as workhorses
Tourney Sets: all 43s >= all 39s > 39s with 43s highest denom NOT in Starting Stack > 39s and 43s mixed