Their recent history with Russia is pretty much the same, yet Lithuania's Russian population is 1/5th of either. Did Russians during the imperial/soviet period migrate there less? Why?
Russians migrated less to Lithuania than the other two Baltic countries.
The Russians moved to port cities to follow trade routes, and until 1923, Lithuania didn't have a port city of its own. It's current port, Klaipeda, was part of Eastern Prussia (and called Memel) until then.
In addition, the Lithuanians weren't absorbed into the Russian Empire until the Napoleonic Wars while the other two Baltic countries were taken a century earlier at the end of the Great Northern War.
EDIT: I probably should point out that the key Soviet decision to make Kaliningrad Oblast part of Russia instead of Lithuania meant that one million Russians are in "Russia" instead of Lithuania. If it were part of Lithuania instead, the Russian demographics of Lithuania would be on par with its fellow Baltics.
According to Ethnic Minorities in the Post-Communist Transformation of Lithuania by Juozas Lakis. The Soviets were encouraged to migrate into other Soviet republics. This especially included the three Baltic States of Estonia, Latvia, and Lithuania.
However after its collapse, Russian migrants ended up trapped within independent republics that were trying to rid themselves of past Soviet control. Latvia, Lithuania, and Estonia all dealt with the immigration, integration, and acceptance of these ethnic Russians in different ways.
The Soviet Union government basically dominated all three countries from WWII up until their independence in the early 90s. Soviet rule forced these countries to give up their sovereignty and succumb to Soviet power. During this period, Russians were encouraged to migrate to these countries to work, and through this immigration process, the number of Russian residents within these countries skyrocketed.
The number of ethnic Russians was extremely high by the time the Soviet Union fell in the early 90s: Estonia with roughly 474,843, (30.3%) of the total population, Latvia with roughly 906,000 (~34%), and Lithuania with 344,500, (9.4%) according to Latvia Looks West, But Legacy of Soviets Remains by Timothy Heleniak.
The central reason Lithuania had lower numbers was because of their already large population and available workforce. The demand for Russian workers was not very high during the Soviet era so not as many emigrated there. Since achieving independence, however, the number of ethnic Russians has declined in all three of the states. This decline is caused mostly by emigration and naturalization. The percentages of Russians in these countries near the start of the twenty-first century had changed to:
Estonia ~25.6% (-4.7% decline)
Latvia ~28.8% (-5.2% decline)
Lithuania ~6.4% (-3% decline)
Despite the three countries all being republics, they have dealt with their large Russian minorities quite differently since regaining sovereignty according to a review labeled under, Lithuania's Russians Feel Least Discrimination in EU. Both Latvia and Estonia perceive the Russian population to be a reminder of their unhappy past and do not welcome these people into their societies despite years and generations of Russians living in these countries. On the other hand, Lithuania deals with this minority group in a very different way. It does not take the Russian minority to be a threat and honors their culture and history as an enriching part of their multicultural society. But that is a story for a different day I suppose.