There can be little doubt that when it comes to influential Supreme Court Chief Justices, John Marshall sits at the top. The rulings of his court were crucial to the expansion of the Supreme Court's power, and the supremacy of federal law.
Having said that, what if Marshall was never appointed Chief Justice? His predecessor, Oliver Ellsworth, resigned due to illness he had contracted after returning from France as Envoy Extraordinary. The POD is pretty simple - Ellsworth avoids his illness, and stays on CJ until his OTL death in 1807. Ellsworth was a Federalist, and it seems likely he wouldn't rule any differently than Marshall on the cases he heard (crucially Marbury v. Madison). But after his death, this changes, as Jefferson will certainly appoint someone from his own faction. Just to get the ball rolling, here are a few choices:
Charles Pinckney (SC): In 1807, Pinckney was serving as governor of South Carolina. He had previously been a prominent member of the state legislature, delegate under the Articles, framer of the Constitution, US senator, minister to Spain, and governor of SC on two other occasions. He had been Jefferson's campaign manager in 1800, which suggests the two had a good reliationship. His views on state religion could have an interesting effect on any rulings regarding it and the law, as well as support for expansion of slavery.
Nathaniel Macon (NC): In 1807, Macon had already been an experienced congressman, having just finished serving as Speaker for the past six years. He was a stauch opponent of Federalism, and an enthusiastic supporter of Jefferson, especially their foreign policy. Jefferson offered him the position of postmaster general on two occasions, but Macon declined, suggesting he might have preferred dedicating himself to Congress and foreign policy. Macon's strong belief in state sovereignty could be quite interesting. If anything like Worcester v. Georgia happens during his tenure, the Indians might have an even worse deal.