Is it safe to let my 3 month old lo lean against the pillow in a sitting position? Understand her neck is not so strong yet, was wondering if leaving her in that position will affect her development?

not recommended yet. for 3mo baby you can focus on training their neck muscles or you can prop them 45deg on a pillow but not on a sitting position. their spine is not ready for such a position until about 5 months old.