Probably because one of them wanted to go with Harry
Parvati and Padme looked at Harry while McGonagall was talking about who could attend the ball. This would suggest that they were interesting in going with Harry.
Indeed, Parvati does later go to the Yule Ball with Harry, and (initially) is rather enthusiastic about it.
“Wait here,” he said to Ron, and he stood up, walked straight up to
Parvati, and said, “Parvati? Will you go to the ball with me?”
Parvati went into a fit of giggles. Harry waited for them to subside,
his fingers crossed in the pocket of his robes. “Yes, all right then,”
she said finally, blushing furiously.
—Harry Potter and the Goblet of Fire
Lavender, Parvati, and Harry are all in the same year, so the statement that "you may invite a younger student if you wish" is probably not relevant. It might seem that it must be, since Parvati and Lavender start laughing as soon as McGonagall mentions inviting younger students, but keep in mind that this is the same sentence in which she announced the Yule Ball in the first place.
One other possibility is that Parvati, Lavender, or both, could be older than Harry by a few months. This note indicates that Parvati was older than Harry, but it is based on the supposition that Padma was taking Potions in HBP, which, based on a text search, does not seem guaranteed. In any case, they could have been appreciably older than Harry, which might explain their laughing at that exact time. On the other hand, they could have been a few months younger, which might also provide a reason. It doesn't seem likely that Parvati and Lavender would consider someone in the same year "a younger student," but it is possible.