Partly because Christianity spread to Scandinavia from Germany and England and Scandinavia spread Christianity to Lithuania/Estonia/Latvia. It wasn't until the 1000s that there were enough organised Christians to lead the Northern crusades. Many of the Northern crusades primarily concerned themselves with areas Sweden and Finland, which were struggling with Christianity but they also extended to other countries.

Before the Northern Crusades, there wasn't a big enough group of strong organised Christians to go to Estonia and the like and kill off the Pagans and convert (especially considering that many of the countries attacking still had many Pagans in their countries). With the aid of German forces, Sweden & Denmark started to move in on Estonia. The same can be said for Latvia & Lithuania although in their case it was mostly Germans who were invading. So, TL;DR: There weren't enough Christians in Northern Europe to convert those countries until 1000s-1300s. Also, many of the countries that could of easily converted them due to their proximity had to deal with the Pagans in their own countries first.

North enough to be among the last ones to be reached, populated densely enough to not have been easily subjugated like the Finns for example.