Here Joseph Smith edited the printer’s manuscript so that the singular was was changed to the plural were (possibly written as ware). Joseph made this change by overwriting the as in was with ere (or possibly are). The w was not crossed out, so he apparently intended to change only the number of the verb form. The 1837 typesetter misread Joseph Smith’s were (or ware) as are.
Generally the text uses the past tense to describe geography in a past-tense narrative. For instance, all other geographical examples involving the word borders are in the past tense, even though in the historian’s time (either Nephi’s or Mormon’s) each of these locations could have been accurately described in the present tense (note, in particular, that the phraseology in the example from 1 Nephi 16:14 parallels 1 Nephi 2:5):
Thus the verb in 1 Nephi 2:5 should be in the past tense rather than the present tense. The critical text will, of course, also restore the original singular verb form was. See the discussion under subject-verb agreement in volume 3.
Summary: Restore the past tense as well as the singular in the relative clause “which was nearer the Red Sea” in 1 Nephi 2:5.