Prior to WWI, what we know of Lithuania today was split among a couple of provinces called "gubernias" or governates of Russia under the Czar.All of Lithuania had been ruled by Russia since the late 1700's until the German army occupied the area in 1915 and ended formally with Bolshevik Revolution of 1917.
One of these gubernias was Vilnius (all were named after the major city in them).According to the Russian census of 1897, the entire governate, including the city, in 1897 had just under 160,000 people, of which more than 55% were Belorussian or White Russian, 17% Lithuanian, and 12% Jews.This census was criticized because the ethnic identity was determined by language spoken.The 1916 census done by the German army for the city of Vilnius showed 140,000 people of whom 50% were ethnic Poles, 44% Jews, and just under 3% Lithuanian.Furthermore, just after WWI, Poland invaded and occupied the southern and eastern part of present day Lithuania, including the city of Vilnius.
So on passenger manifests, emigrants would often use the name of the gubernia as their last residence or birth place.The actual village or town they were from might be something quite different, just as someone in the U.S. might say they are from New York, meaning the State, when specifically they were from Troy.Secondly, Vilnius only became part of Poland after WWI, though you can see how difficult it would be for ordinary residents without radio or TV or perhaps even newspapers to know precisely where the boundaries of their homeland might be or even who controlled it.Because of the intermingling of ethnic Lithuanians with Poles, Russians, Germans, and Belorussians, many of them spoke more than one language and their first language might actually be something other than Lithuanian.
Almost all of the birth, marriage and death records from the late 1700's to the early 20th century, certainly in the area of present day Lithuania (including the city of Vilnius) were moved to the central Historical Archives of Lithuania.If one knows the name, birth year, and specific town or village or parish, one can request a translated copy of the records from the Archives.Or one can hire a private researcher to do extensive research into the records of one's ancestors -- as I did.My researcher found hundreds of records of ancestors for the years 1750 - 1930.There are some records which have been destroyed or lost.Very few are held by the original RC churches that created them.
A Google search on the history of Vilnius will probably get you hundreds of web sites with varying degrees of detail, including photos.The Jewish Genealogy site www.jewishgen.org is a treasure trove about daily life in Lithuania around the period you are talking about.
If your ancestors came from the area west of Vilnius (Suwalki), it is possible that the records might be held by the Polish central archives.Both this institution and the Lithuanian Archives have web sites.
By searching the web, I have been able to find detailed stories of life in Lithuania in and around the areas from which my ancestors came.