I'd take a 5-year-old to Legoland over Universal any day.
Not only does Legoland have more rides geared towards little kids, it is set up in such a way that every "big" ride has a smaller ride or playscape right next to it. I took 2 big kids and 1 little kid (almost 4) two years ago. The younger one could ride most things, but when she couldn't (or didn't want to) ride something, there was always something else nearby.
Universal has two kiddie areas, one in each park, that kind of concentrate the rides for little kids. There are other rides scattered through the park that are good for the whole family, but some of them are intense enough that your son might not enjoy them, even if he meets the height requirements. This spring we took a trip to Universal. DD was almost 6, and she loved it, but we spent a fair amount of time utilizing rider switch, and splitting up. There were rides she COULD have gone on from a height perspective, but they were too scary - some she went on and screamed and vowed never again, and others she flatly refused to try. YMMV with the adventure level of your child.
Universal was a great trip, but to me, it feels geared more towards older kids and adults, with some kiddie things thrown in so as not to exclude families. Legoland is designed with little-to-medium kids in mind, and your son is the perfect age. I think your family could absolutely have a fun time at Universal, but I think your son is the targeted demographic for Legoland, and would get more out of it. Coupled with the price difference (which is even better when you use a BOGO coupon for his ticket), Legoland is probably the better choice for this trip.
It is a fairly small park, compared with Disney and Universal. One day is enough to do it, unless you buy a combo ticket and spend a lot of time in the waterpark.