The relative clause originally had the singular verb form is. The antecedent for which is “the first”, probably meaning “the first records”. The plural is actually found at the end of the previous verse (“the records of the prophets and of the twelve apostles of the Lamb”). Nonetheless, there are many instances where the original text interchangeably refers both to “the record” and “the records” (for a list of examples, see 1 Nephi 5:21). So “the first” here could be referring to ‘the record’.
Such shifts in number frequently occur when there is some intervening text between the relative pronoun and its antecedent. Here in 1 Nephi 13:40, the immediately preceding noun phrase is in the singular (“the truth of the first”), which may have been the reason why the verb in the relative clause is in the singular. Similarly, in the following example involving records, the singular Limhi occurs just before the relative pronoun which, thus influencing the choice of the singular was in the following relative clause:
For further discussion of the effects due to proximity, see subject-verb agreement in volume 3.
Summary: In accord with the earliest text for 1 Nephi 13:40, restore the original singular verb form is in the relative clause “which is of the twelve apostles of the Lamb”.