Oops, It looks like I got the rooms mixed up.
So the generator you're talking about is the one that is next to the room where you had to push a block on a switch to keep the windows open. These windows you could climb up out of. The one on the left has a ladder going down and the one on the right should give you access to the dinghy.
To get to the generator, you need to shift time to the present to disable those beams. However, you needed to be in the past to get to the room in the first place. You need to shift back to the present from there. How do you do it?
Well you need to lower the dinghy so you can reach the deck and hit the crystal. From that room, it would be easier to just climb out the window with the ladder, go down and and look toward the other window and up at the deck. You should see the dinghy there with a target to hit. Hitting it will lower/raise it.
After you had lowered it, you can return and climb onto it and hit the target again to raise you to the deck. From there, shoot the time crystal to shift to the present. Then you could return to that room using the dinghy and to the generator. Now you need to shift back to the past again so you can activate the generator. Fortunately there's a grate above with a clear view to the time crystal. Shoot it so you can shift to the past and finally activate the generator.
To get to the second generator (the one in the south), start off from the first generator.
You'll notice that the room across the hall on the left has a fan in there. If you are in the past (everything is colorful and operational), the fan should be spinning. Inside that room, you should see a blue switch that you'd have to shoot at. You cannot shoot through the fan when it's off so you need to go to the present (where everything is dull and not working) and shoot it then. That should open the door to enter the room (IIRC).
In the room there should be a switch on your left and bars on the right looking into the next room with a box sitting on a platform. The switch opens a hatch that covers a target that you have to shoot at however you don't have a direct line of sight to it since the box is in the way. You'll need to move the box over so you have access to the fan behind it. You need to open that hatch and shoot at the target. With the box out of the way (and the fan off), you should be able to do so. It should open the gate leading to that room.
Now you have access to the generator so you just have to go back into the past where it's operational and turn it on. You can access the crystal back in the room with the previous generator.
Best Answer
There are 3 different approaches I have to go against them with varying degrees of success.
The best and easiest way to handle them is to use a shield and Shield Bash them as they attack. That will daze them for a while so you could counter. Their heads should be lined up by then. Note that if your shield is weak and about to break, a shield bash will not damage it.
Another way is to use the Skyward Strike on them. You just have to slash in the orientation that their heads are in. This one isn't too reliable as you have to anticipate their moves (and need some luck).
Probably the hardest way to deal with them is to fight "head-on." When they're about to strike, their heads will be oriented in a certain way. If you have a fast enough reaction time and close enough to attack, you could slash in the same orientation to kill them off. A more cautious approach would dodge back first when they do attack and counter. I don't remember what their orientations are after they attack but it will probably be in the same as when they attacked or horizontal. You may have to experiment with that.
Probably the least successful way to deal with them would be to randomly attack them. Their heads will mostly be not lined up so you won't be able to kill them that way. Wait for them using the tips above to kill them.