Yes he was. William Clark was a lieutenant-captain and was in fact Lewis' superior prior to the expedition. However, once Jefferson assigned Lewis to the expedition, Lewis was promoted to Captain. Lewis always considered Clark his "co-captain" and kept secret the fact that Clark was of lower rank from the other members.
Below are links to two separate WikiAnwers questions, that will answer this one: Long list of plant life discoveries by the Lewis and Clark expedition: http://wiki.answers.com/Q/What_plant_life_did_Lewis_and_Clark_find_on_their_expedition Long list of geographical landmark discoveries by the Lewis and Clark expedition: http://wiki.answers.com/Q/What_geographic_landmarks_did_Lewis_and_Clark_encounter&updated=1&waNoAnsSet=1