There is one obvious way those eggs could have gotten aboard the Sulaco, but it's not one most fans will want to consider.
Bishop could have brought them aboard. Remember that he was supposed to wait with the drop-ship while Ripley went to rescue Newt. But when she returned to the rendezvous point, he was gone. He returned shortly thereafter, explaining that the landing platform had been too shaky to remain on.
This leaves a good ten to fifteen minutes during which he was unaccounted for. He could have easily used that time to locate the hive, retrieve a couple of eggs, and stow them on the drop ship before returning to pick up Ripley.
This obviously makes Bishop a traitor, a fact that won't sit well with most fans of the franchise. But of course, he is Weyland-Yutani property. There's no reason he couldn't have been programmed with the same "crew expendable" bias as his predecessor on the Nostromo. In his defense, he might not have even been aware he was doing it.