Blacklegged ticks (Ixodes scapularis Say, Acari: Ixodidae) are the most commonly encountered and medically relevant tick species in New York State (NY) and have exhibited recent geographic range expansion. Forests and adjacent habitat are important determinants of I. scapularis density and may influence tick-borne pathogen prevalence. We examined how percent forest cover, dominant land cover type, and habitat type influenced I. scapularis nymph and adult density, and associated tick-borne pathogen prevalence, in an inland Lyme-emergent region of NY. I. scapularis nymphs and adults were collected from edge and wooded habitats using tick drags at 16 sites in Onondaga County, NY in 2015 and 2016. A subsample of ticks from each site was tested for the presence of Borrelia burgdorferi, Borrelia miyamotoi, Anaplasma phagocytophilum, and Babesia microti using a novel multiplex real-time polymerase chain reaction (PCR) assay, and deer tick virus using reverse transcription–PCR. Habitat type (wooded versus edge) was an important determinant of tick density; however, percent forest cover had little effect. B. burgdorferi was the most commonly detected pathogen and was present in ticks from all sites. Ba. microti and deer tick virus were not detected. Habitat type and dominant land cover type were not significantly related to B. burgdorferi presence or prevalence; however, ticks infected with A. phagocytophilum and B. miyamotoi were collected more often in urban environments. Similarity between B. burgdorferi prevalence in Onondaga County and hyperendemic areas of southeastern NY indicates a more rapid emergence than expected in a relatively naive region. Possible mechanistic processes underlying these observations are discussed.