Yes, the e-Visa for India can now be issued for arrival at designated seaports. Since the extension of validity of e-Visas, your cruise can dock at as many ports in India as required, as long as the e-Visa is still within its validity period.
 Beware, some companies, unaware of this handy e-Visa, often impose a traditional visa. A good way for them to sell it at a high price