This depends on your criteria but there is a strong case for either side.
They both have 17 league titles since the inception of the current league format (in 1959), but overall Fenerbahçe holds 26 national titles to Galatasaray's 18. However, Galatasaray holds more cup titles and has a UEFA Cup to their name as well.
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So about your question.
Galatasaray is FAR MORE BETTER team than fenerbahce. with 17 Super league trophies, 14 Turkish cups and 2 European cups
Fenerbahce has 17 Super League cups, 4 Turkish cups and none European.