It's mostly a result of internal politics within the Land Diet, as well as the Jagiellon's own diplomatic maneuvering during and after the death of George of Podebrady/Jiří z Poděbrad.

King George had spent most of his reign delicately balancing the post-Hussite situation in Bohemia, which included how to go about handling interventions into the Bohemian crownlands. King George's main focus beyond the Holy Roman Empire itself was a building a relationship with Kazimierz IV Jagiellon in Poland. Lastly, he worked to focus the anti-heresy energy within Christian Europe against the Ottoman Turks instead of his own domestic religious schisms. But those religious divisions within Bohemia caused fighting to break out at times and this led to another anti-Hussite crusade in 1468. This crusade was led by the Hungarian King Matyas Corvinus, who had been offered the crown of Bohemia by a group of anti-King George Catholic nobility called the League of Zelená Hora. And this conflict was going on when George of Podebrady died in 1471.

After King George's death, Bohemia was left in very close contact with the Jagiellon dynasty and with historical grievances against Hungary, whose ruler was currently laying claim on the Bohemian throne. The Jagiellon's had also been preparing to win a post-George election to the Bohemian throne for a long time. Kazimierz IV had used King George's weak position at the end of his life to convince the Czech king that he should not name an heir, as well as accept a Jagellion on the throne. The Hungarian king Matyas - who still claimed the Bohemian throne - also put himself forward as candidate. The Bohemian Diet, comprised of the Bohemian Estates, chose the Jagiellons.

So, to finally get at the heart of your question, the Bohemian Diet prefered the Jagiellons because that seemed like the best option for preserving all the priviledges and autonomy they had won for themselves over the last half-century. The Hungarians were at the helm of a crusade against Bohemia, while the Jagellions had been more open to negotiations with the Utraquist nobility and respecting their autonomy. Since electing a foreign ruler didn't matter much back then and no single lord within Bohemia at that time was powerful enough to become king (or wanted to in the first place), the choice was made between dynasties from the two neighboring kingdoms.

Source: Jarosláv Pánek et al., A History of the Czech Lands, Prague: Karolinum Press, 2009.