I wouldn't render the imperfect ἦν as a pluperfect (and you seem to have missed ἑστηκώς) "The next day the crowd standing on the opposite shore saw that there was no other boat there except one, and that..."
It's a bit of a stumbler, though, because one naturally asks the question "what boat is he talking about?" and that's precisely what we see in the manuscript tradition:
{A} ἕν 𝔓75 א2 A B L N W Ψ f1 157 205 565 579 1010 1241 itaur, (b), c, f, ff2, l, q, (r1) vg coppbo, bo, ach2, mf eth slavms Augustine // ἓν ἐκεῖνο εἰς ὃ ἐνέβησαν οἱ μαθηταὶ αὐτοῦ (א* f13 l 547 copsa τοῦ Ἰησοῦ for αὐτοῦ) (Δ ὅν for ὁ and ἀνέβησαν) Θ 0141 28 180 597 700 892 1006 1243 (1292 l 1070 ἀνέβησαν) 1342 1424 1505 Byz [E F G H] Lect (itc) syr(c), (p), h, (pal) slav Cyrillem // ἓν εἰς ὃ ἐνέβησαν οἱ μαθηταὶ αὐτοῦ (D* αὐτοῦ Ἰησοῦ) (Dc ita, d τοῦ Ἰησοῦ for αὐτοῦ) 33 1071 l 68 l 184 syrs (arm) (geo) (Chrysostom)
Aland, B., Aland, K., Karavidopoulos, J., Martini, C. M., & Metzger, B. (Eds.). (2014). The Greek New Testament: Apparatus (Fifth Revised Edition, p. 328). Deutsche Bibelgesellschaft; American Bible Society; United Bible Societies.
Metzger explains:
In order to clarify the evangelist’s statement about the boat, copyists added, in one form or another, the explanation that it was the one “into which his [Jesus’] disciples had entered.” The variety of wording of the addition condemns it as secondary, just as the age and variety of witnesses which support the shorter reading confirm that as original.
Metzger, B. M., United Bible Societies. (1994). A textual commentary on the Greek New Testament, second edition a companion volume to the United Bible Societies’ Greek New Testament (4th rev. ed.) (p. 181). London; New York: United Bible Societies.
N.E. Barry Hofstetter
Cuncta mortalia incerta...