It seems deeply unlikely that Queen Amidala wouldn't know exactly what a Gungan is. In this scene she's trying to cement the idea that her alter-ego, (the palace handmaiden Padmé) isn't especially worldly and perhaps a little bit naive.
“Mesa JaJa Binkssss,” Jar Jar said.
“I’m Padmé,” the girl told him. “I attend Her Highness.” She looked at him curiously. “You’re a Gungan, aren’t you?”
Jar Jar nodded. Most Naboo didn’t like Gungans any more than Gungans liked them, but this girl seemed nice. And she not yelling over little mistakings, like everybody else.
Star Wars: The Phantom Menace - Official Novelisation
As far as the charade is concerned, the novel also makes it clear that Naboobians and Gungans don't typically mix. They live in different climes and have very little in common. Trade between the two races is solid, but conducted largely through intermediaries and it, presumably wouldn't have been unheard of for a Naboobian to never see, let along meet a real life Gungan.
On top of that, there's the fact that most trade contact is done by the ruling Ankura Gungans (of which Boss Nass is a prime example) rather than the majority Otolla Gungans (such as Jar Jar). Even if you'd ever met an Ankura Gungan, you might not recognise an Otolla Gungan as being from the same species.