When a question for skaven starts "what's the best unit to use against _________________ ", the first answer is almost always:
Warp Lightning Cannon. Accurate, deadly, template, no armor saves, multiple wounds. It is pretty much the best option for whatever needs to die, generally speaking.
Second answer:
Another Warp Lightning Cannon.
Seriously though, ranks of clan rats or slaves to hold up the enemy are always good. Chaos and HE both tend to have units that a Plague Mortar works well against. It ignore armor saves and always wounds on 5+. Wonderful against Chaos Warrior for the armor save denial.
Lore of Plague Spell: Plague. T test or die is great against HEs. Against Chaos Warriors, you might need to hit them with Wither a few times to lower their innately high T.
Against either army, Crack's Call is definitely of lower value. Both armies have high I models who will easily make their tests. Howling Warpgale is useful against HEs, especially for saving your war machines from Great Eagles. They may fly, but with Warpgale up they're moving at a whopping M2.
Poisoned Wind Globadiers will actually make their points against Chaos Warriors, as once again they ignore those pesky armor saves and have a flat to wound roll regardless of enemy T.
Against HEs, the Plague Claw Catapult may stand out. The large template can hit entire blocks and their low T means you have a better shot at wounding. Still not terrible against Chaos, but you'll probably be able to find a better use for the points.
HPAs I find are hit or miss. They either do extremely well, or they die on impact. Your mileage may vary.