No other choices? There were at least four major candidates that year.
Our electoral system before 12th amendment was pretty screwed up. Thomas Jefferson and John Adams were the only presidential candidates, and the only ones voters could actually vote for. All the other candidates were vice presidential candidates that electors picked with their second vote.
There were machinations to elect Pinckney, and in 1800, there was a decent chance Burr would become Adams' successor.
I actually explained that a bit wrong (edited post), every elector was for president, but don't ask me why there were only two or one people on the ballot for voters to actually vote for in these times. In 1800, Burr and Jefferson tied in electors, and Jefferson became president by a house vote (which also means Burr became vice president). The only ones voters could vote for were Jefferson and Adams.