Warmongering early to take cities is hard. You have to put a lot of hammers into an army, and the AI can support a bigger one then you can. Also, taking cities is quite hard before siege units become available, then you have to build them, and if the war drags out it can start really hurting you. It's a gamble I'd say, and even if you succeed it will jack up your warmonger score if you know a few other ppl. Early puppets are also annoying as you need to micromanage to make the most out of your cities in the beginning. You can't control their growth without some careful landscape sculpting, and before trade posts (much later) this basically means leaving them unimproved. A captured capital can be bad--They can't build military, they will grow uncontrollably, which often means it'll stunt your own capital and cause happiness drains. Might work for a start if you intended domination but probably wouldn't help with a science victory. I tried it once with Shoshone with 3 early CB's from ruins and stole eithiopia's capital. But even knowing just 2 other AI this caused a string of DOWs and made me delay NC, and the city grew so fast it nerfed my capital--it was a frustrating game.
Now: This doesn't mean early war can't help your science, but happiness is so short and puppets kinda inefficient for science. So really, early war where you take cities before you can handle them is really the problem. However, I've had success with early economic wars. Just don't worry about taking cities, declare war on some neighbor before you know hardly anyone (almost no warmonger hit). Then steal their starting workers, pillage their land, and keep the war going, taking settlers, destroying trade routes, and getting more free workers over the course of time. The super-early workers gives you a huge early growth boost as AI get workers before anyone else including CS on high levels and it removes their advantage and gives it to you. It also cripples a neighbor and helps give you more room. This strategy is more effective the greater the AI advantage as they'll be throwing workers and settlers and trade routes out almost immediately on immortal/deity so you have a lot of free stuff to capture. Pillaging will also give you gold. On a deity game as Aztecs I built 2 jags plus my starter (a tiny opportunity cost as they were also my scouts) and laid into my closest neighbor with some hit-and-run tactics. I stole 2 workers, a settler, pillaged a trade route, got a lot of experience, and pillaged 5 tiles. By the end of the war I had 3 free workers, about 200 in stolen gold (about half a library or settler), had 3 high-lvl jags, and had set back my neighbor giving me enough time to take my time placing 4 cities. It was great. Best part was I got virtually no warmonger hit as I DOWed only knowing him. I qickly met everyone else but they don't care if you are fighting someone only about DOWs and taking cities so I got no warmonger score for the act except with the target. He was even a friend later because I didn't take any cities. It was hilarious.