99,
400 Chevy "small block" (there are two 400 Chevys, one is really a 402 BB, but called "400" in GMC trucks, early '70s) has a bore of 4.125" and a stroke of 3.75". It uses standard deck height and bore spacing of the small block (ala 350 Chevy). It also uses the 17-bolt heads typical of 350 Chevy.
400 Pontiac is a completely different animal, and virtually zero of the parts interchange. 4.120" bore and 3.75" stroke. It has a much taller deck height and a longer connecting rod. The heads use 10 head bolts (1/2" vs. 7/16" for the Chevy). The bore spacing is "bigger", falling right between BBC and SBC.
In stock form, the small block heads have an okay intake port and a good exhaust port. With a little work, they SHINE! That is, the small block Chevy has among the best flowing (per size) heads out there, once modified or replaced with aftermarket.
The Pontiac has a much better intake port, stock, but the exhaust port is woeful, and that's being kind. With significant porting, the stock Pontiac can be a good head, but the Chevy is probably a bit better with the same level of porting. As with the Chevy, aftermarket parts change everything.
Where the two engines differ the most (aside from durability, and we'll touch on that in a minute), is how and where they make their power. The Chevy, as with most small blocks, works best when it's revved a bit. Usually to about 7,000, but with some "real" goodies, we've built 'em to go well over 8,000. Low-end torque is better with 400 than any of the smaller ones, but that's the displacement at work. It's still a bit "shy" when it comes to serious torque, compared to other 400 CID engines.
The Pontiac's strong suit is the opposite. It makes power right off idle, and can pull hard to about 5,200 in stock form (350 horse and better). Due to the shape of the intake port and the rod length, the Pontiac 400 out-torques all other GM 400 CID engines of the era. When certain modifications are made, it can also rev up pretty good, and make good power. We usually limit them to the 7,000 range unless MEGA-bucks are spent on bottom-end pieces.
Which is "better"? Depends on your application. I like Pontiac engines in Pontiacs, but I also like Chevy engines in Chevys! If you're building a street engine for "fun" and not too serious, the Pontiac has an edge due to the torque production and low-speed performance (GTO didn't earn its reputation from losing). For a "race" engine, if all the bases are "touched", the Chevy is probably a skoche better.
Which is tougher? The Pontiac, no doubt. Now, small block guys, don't wig out on me here. Hear me out. If we were comparing 350 Chevy to 400 Pontiac, Chevy is a tougher engine, especially when pumped up with mid-level parts. But 400 is NOT 350. The bores are too large, requiring "siamesed" cylinders (no water flows between them). The main bearings are also too big for the original design of the block. Due to this, a 2-bolt main is desired over a 4-bolt (unlike 350), if stock. Chevrolet never produced a stock-block "performance" 400. This is why. When using an aftermarket block, everything changes. The connecting rod in the Chevy is also too short for the stroke. The Pontiac has a definite "edge" there. When we build 400SBs, we ALWAYS install 6" rods if the customer will spring for them. The 350 5.7" rod is an improvement over the 5.565" 400 rod, but still not enough. The Pontiac uses a 6.625" rod.
Anyway, I hope you get the idea. For some of the younger crowd today, there's a LOT of confusion regarding the GM engines of the muscle car era. Each division had it's "own" engine family until the mid '70s. Buicks are unique, as are Olds, Pontiac, Chevy and Caddy. They crossed "lines" once in a while, but were usually independent. All 4 of the main divisions had a 350 CID engine. None of them were even similar. None have the same bore and stroke combination. And not all of the 350s were "good" performance engines. Actually, the Chevy is a far better performer than the others, with the Olds coming in "2nd". Once CID approaches 400, small blocks begin to fade, especially in stock form.
NOTE: There's no such thing as a "small block Pontiac" OR a "big block Pontiac". There is the "Pontiac". Same deck height, bore spacing etc. from '55 through '79, with displacements ranging from 287 in '55, to 455 in '70. The only parametric difference besides bore/stroke is the main bearing diameter. They all even use the same rod length. A notable exception is the bastardized 265/301 Pontiac. It has a MUCH shorter deck and uses Buick-style rods and Chevy valves. Wierd little engine. Not much "account". The crank is too wimpy to be useful.
Helpful?
Jim