The exact answer: yes, 4.88 is stronger. By how much... the difference is probably negligible. I have heard people say to stay away from 5.71 toyota gears... but that's anecdotal at best... if you want 5.29's, run 'em, and don't worry about strength issues compared to 4.88's.
I have had both 4.88's and 5.29s. I am not a rock crawler guy but I gave my truck hell spinning 35's and I haven't broken the 5.29s. But yes the 4.99s are stronger.
4.88's are stronger. Toy r&p's fail at the pinion 99.99999% of the time my experince dictates. A toy 5.29 pinion has 7 teeth. A toy 4.88 has 8 teeth. I'l tell you how they hold up after abusing a set of yukon 4.88's in my wife's 4.3L powred 4 runner soon :awesomework: