Yes, "it" is singular. It refers to the "logos". "Logos" was the Greek word used for the Hebrew "dabar" as in Jeremiah 1:4-5;
Jer 1:4 Then the word [Hebrew dabar; Greek logos] of YHWH came unto me, saying,
Jer 1:5 Before I formed thee in the belly I knew thee; and before thou camest forth out of the womb I sanctified thee, and I ordained thee a prophet unto the nations.
Did a single "word" come to Jeremiah or did many words come to him that were categorized as a singular word? Verse 5 shows that many words came to Jeremiah. "Logos" is a singular noun that can refer to more than one word. Logos, as used in John 1:1, refers to the Father's thoughts, plans, spoken words all summed up in the pronoun "it" in verse 3.