While losing 1000 tons of ground units, I only managed to destroy 3x elite infantry, 1 resupply unit, and 1 anti-tank team,
What happened is that the ship you attempted to board was a troop transport, and troops on a troop transport will fight back during a boarding action. 1,000 tons of infantry against ~25,000 tons of spoiler-level invasion troops will basically never end well. Against anything that's not a troop transport you probably would have been okay.
This being said, you should be aware that due to how boarding combat
usually works (i.e., when the enemy ship isn't crawling with angry space marines), PWI is a very poor choice of weapon for boarding parties. During boarding combat, crews are modeled as INF+PWL with half the racial tech level in armor and HP, which means that if you have equal tech PWL is the best weapon for your boarding parties, and even against an enemy with superior tech PW or CAP are more than enough to penetrate and kill in one hit. In almost any reasonable scenario, PWI is just wasting valuable tonnage that could be used to cram in more, smaller weapons that would do the job.
I would generally recommend using PWL+CAP for boarding parties, even against higher-tech enemies the PWL act as effective meatshields for the CAP which will do most of your damage.