[ Historically, the Lenape inhabited lands that are now parts of New
Jersey, Pennsylvania, Delaware, and New York ], and [ they settled along
the rivers and bays ].
This is a compound sentence consisting of two independent clauses. Compound sentences are linked by coordination, usually with one of the coordinators "and", "or" or "but".
Note that the relative clause that are now parts of New Jersey, Pennsylvania, Delaware, and New York is a subordinate clause in noun phrase structure, not in clause structure, so it has no relevance to the status of the sentence as a compound one.
I've bracketed the two independent clauses.