The use of the solar eclipse to prove a claim to supernatural power
was not a new concept when Twain wrote CY.  In the Iowa/California
edition of the WORKS OF MARK TWAIN, edited by Bernard Stein, (p. 553)
Stein points the reader to THE LIFE AND VOYAGES OF CHRISTOPHER
COLUMBUS, Book 16, chapter 3 by Washington Irving.  (Columbus
exploited an eclipse to get natives to procure supplies for him.)
Clemens owned a set of these books in the 1880s.

Louis J. Budd in MARK TWAIN: SOCIAL PHILOSPHER, p. 134 suggests H.
Rider Haggard's KING SOLOMON'S MINES (1885) as an inspiration.
Haggard's book got further publicity from an argument over whether an
eclipse that its heroes exploited was astronomically on time.

Howard Baetzhold in MARK TWAIN AND JOHN BULL (P. 346-347) discusses
the possible influence of THE PRAIRIE FLOWER (1849) by Emerson
Bennett. In that book, the heroine "invokes" an eclipse to insure her
safety.  Baetzhold suggests Twain may have seen the stage production
of THE PRAIRIE FLOWER during the 1870-71 season at the Bowery Theatre.

The eclipse concept, without regard to historical accuracy, was not a
new plot device when Mark Twain wrote CY.