Geography plays a role, Vermont was better suited to Agriculture and New Hampshire not as much, though New Hampshire was well suited for industrial production.

With agriculture, fewer people tend more land, and your hamlets and small towns develop accordingly. With industry and manufacturing, you need more people to work in a focused area and develop larger towns and small cities. Vermont's larger towns and cities tend to be a result of commerce (shipping, railroad hubs etc).

Brave Little State did an interesting piece on the development of the two states years ago.