1: Maxed Paranid reputation. Pretty obvious here, since boarding will cost you 2-3 ranks even at max rep; it's far easier to repair rep when you aren't going to be shot on sight by the locals, and it means your newly acquired ships aren't going to be hammered by their former friends.
2: OTAS Sirokos. Fastest M7M, and the ability to carry more than 20 marines means you can train more of them at a time (at least vs. the Agamemnon)
3: Isolation. Your target ship needs to be as close to alone as you can get it. The Agamemnon is more likely to be found with escorts, including M8s. I've had them with 2 Hades in the past, destroying them will hurt your rep further than you need to and can turn the Agamemnon hostile before you're ready and generally make things more difficult in general. There will be several around Paranid territory at any one time so you don't have to go after the first one you find. The Hyperion is more likely to be found all by itself and I've yet to get one that's had fighters docked inside.
Rule of thumb is that any ship that's labelled as "Paranid military" or any variation is going to turn hostile on you when you pick your fight, as a result it's better to avoid core sectors since they'll be more likely to feature capital ships and you don't want those breathing down your neck
As for what ship you fly to suppress shields, for the Hyperion I recommend the Springblossom, it has the blend of firepower and speed that will be very useful. I use 6 M/AMLs initially, then 2 SSCs to keep the shields down, then the speed to get away quickly once my marines are onboard.
For the Agamemnon I recommend the Split Tiger for the same reason, 2 or 3 charged blasts of IBLs will strip shields effectively (depending on what shields the M7 spawned with) as long as you're close enough to make sure you don't miss due to the speed of the projectiles. They'll also not cause the target to turn hostile until you've stripped most of the shields or the pods launch, whichever happens first. While it can't outrun its counterpart as fast as the Springy can, its shields can withstand fire for longer and in the hands of a skilled pilot can avoid a lot of fire.
For both ships I recommend turning off your turrets when you do the initial attacking since they'll likely inflict unnecessary hull damage. You'll want to have your Sirokos follow you to the target then loiter 5-10km away so that they're out of weapon range but close enough that boarding pods will still arrive quickly. You'll want to keep the target focused on you to start with so that your pods are less likely to get shot down.
Once your troops are onboard it's the usual procedure of running towards the nearest gate (or jump if you need to), and having your Sirokos jump away if it's too close to the target for comfort until it's under your control. Remember to pick up your extra marine if you used the +1 rule, though if your Sirokos is nearby when you take control he'll fly back to it automatically.
This last bit is where the high initial rep comes in handy, since your new acquisition will be very vulnerable. Order it to fly to the nearest shipyard and jump your own ships out of sector, what you should notice is that the Paranid ships IS won't attack your new ship when you leave (though they will destroy any navsats they find while you are IS). After that, do missions to repair your rep, rinse and repeat. I've boarded a dozen Hyperions using this method, and the cost is minimal