I've built both for my 4runner and used each setup for over a year on numerous long and short duration trips, so I think I am uniquely qualified to answer this questions with my OPINION. haha.
Boxes.
The drawer was great, especially one single large drawer as I built mine, plenty of versatility within the drawer, and held lots of things. But ultimately it doesn't hold EVERYTHING you are going to bring on any given trip, so you logically prioritize leaving in it things like tools and recovery gear. This means that you're still using boxes for things like food, cooking, etc. Meanwhile, you are lugging around all of your tools and recovery gear everywhere you go, taking up space, hurting fuel economy, etc. The Beauty of Totes is the ability to categorize their contents and only brings the one(s) necessary for the trip.
I have Four Boxes: Camp, Kitchen, Tools and Recovery along with my cooler and usually a grocery bag full of dry goods.
Going wheeling for the day, but not spending the night? Tools and Recovery
Going camping somewhere that doesn't required 4wd? Camp and Kitchen
Road Trip? Tools
Picnic at the park? Kitchen
Now, the keyboard warrior/overland bound member would tell you that you should bring everything, all the time, you never know when a trip to starbucks can turn into a Recovery Situation.... but I live in the real world.
Furthermore, I picked the wolfpacks as my box of choice for two reasons, first is that they are small enough that when full of tools, they are not too heavy. Second, four of them fit perfectly in the cargo space of the 5th Gen 4runner.