We saw Naomi's helicopter crash into the sea. No way there is room for two helicopters on this boat.
Either they transferred in a new chopper after the loss of the first (doubtful, due to the nature of their search as we understand it and time constraints), or there is another ship floating around out there with them.

Actually I was thinking of this too when we first see the ship. I recall there being two landing pads for helicopter on the deck of the ship. Of course one of them is now empty.

I always thought that perhaps Charlotte's helicopter didn't crash, that was a cover story, she parachuted onto the island and the helicopter returned to the freighter. Because pretty much everything Naomi said on the island was a lie. So I think that there is only one freighter.

Actually I was thinking of this too when we first see the ship. I recall there being two landing pads for helicopter on the deck of the ship. Of course one of them is now empty.

There are definitely two places to land there, but clearly not enough room for the two. One barely fits.

There's PLENTY of space for two, especially since Lapidus landed his chopper so the tail is hovering over the water.

Just watch the scene when Keamy comes running towards the helicopter. Plently of space for another one.

DarkUFO posted this screencap showing room for two helicopters:

DarkUFO screencap (http://bp2.blogger.com/_pG1kU-zfuxM/R8eA9gnj8bI/AAAAAAAAAGs/q9w8nAuZ3uI/s1600-h/screen-capture-2.jpg)

If it did crash, was there other people on it? There must have been a pilot. Did Naomi at any point express concern for any other potential survivors of the crash? I don't recall her doing so but I could be wrong. And nobody else from the freighter has mentioned anything about losing other people.

I always thought that perhaps Charlotte's helicopter didn't crash, that was a cover story, she parachuted onto the island and the helicopter returned to the freighter. Because pretty much everything Naomi said on the island was a lie. So I think that there is only one freighter.

I'm confused - when you say Charlotte, do you actually mean Charlotte or do you mean Naomi? Charlotte's helicopter was the same one that Miles & Daniel were in, with Frank piloting, right? The one Frank safely landed in the clearing because he's that kind of pilot. ('What kind of pilot do you think I am?:))

Didn't Desmond, et al, see Naomi's helicopter crash into the ocean? I thought they saw her parachute out and then saw the heli fall into the water....

It makes sense that there were 2 helicopters and now there is only 1.

Unless I'm missing something.....
100%
Or, maybe somehow it DIDN'T crash, and Brandon and Minkowski were with her and managed to get back to the freighter. We haven't met Brandon yet, maybe he is out in the other one...

I'm confused - when you say Charlotte, do you actually mean Charlotte or do you mean Naomi? Charlotte's helicopter was the same one that Miles & Daniel were in, with Frank piloting, right? The one Frank safely landed in the clearing because he's that kind of pilot. ('What kind of pilot do you think I am?:))

Didn't Desmond, et al, see Naomi's helicopter crash into the ocean? I thought they saw her parachute out and then saw the heli fall into the water....

It makes sense that there were 2 helicopters and now there is only 1.

Yes, I meant Naomi, don't know why I I typed Charlotte. I thought that because it was Naomi's job to get the team in safe she was supposed to go in first to prepare the way. Her story that her helicopter crashed was the prearranged cover story. If I recall correctly Desmond, Charlie, Hurley, and Jin did hear a helicopter, there was the red light descending to the island, but I thought that was Naomi's transponder beacon which did glow red. I think we have to take everything Naomi said on the island including the helicopter crash story as suspect because she was lying about being sent by Penny. It didn't go as planned for her because she got speared by a tree branch and knifed by Locke(but I think the island doesn't want the freighties there and is doing everything it can to prevent them from accomplishing their mission-look at all that's gone wrong for them can't say the mission is going according to the plan). And like you said, I think Lapidus was selected because he seems to be an extraordinary pilot, I don't think he would have crashed into the ocean. I think it is the only freighter, for now, their communications equipment is down and they can't communicate with the outside world, they can't get their orders and they can't radio their position to their people in the world. So Michael knew what he was doing when he disabled the equipment.