A number of Rishonim quote from Makkot but call it Sanhedrin, implying they considered them to be one tractate. See Ramban to Devarim 21:13 and Rashba to Kiddushin 22a who refer to what we have in the Yerushalmi of the second chapter of Makkot as "פרק בתרא דסנהדרין." Also check out Ralbag to Shemot 21 (Shoresh 4 and 16) who calls our second chapter of Makkot "פרק יג דסנהדרין". (Ralbag also counts them as a single Masechta called Sanhedrin in his introduction to his Peirush on Chumash.)
These are both technically later than the Rambam cited in user6591's answer, but just to add a possibly earlier source, the Midrash Rabbah (Shir HaShirim 6:8 and Bamidbar 18:17) notes that there are 60 tractates [of Mishna], while we have 61 (counting the three "Bava" tractates as one). The Rashash to Bamidbar Rabbah there suggests that this could indicate that Makkot was a part of Sanhedrin at that time. Not an ironclad proof of course, but still worth mentioning.
The Rambam is correct though that there is early manuscript evidence for the joint presentation. The famous Kaufmann manuscript of the Mishna presents Makkot as chapters 12-14 of Sanhedrin. Consider too the incomplete Geonic commentary from the Cairo Geniza (Ginzei Shechter 2 pg 395) which actually combines the chapter אלו הן הנחנקים with כיצד העידם into one long chapter. It's not entirely clear why the Rambam so opposed the notion that they were originally one tractate given all the evidence, the similar topic and style, and the unusual length.
To be fair the Bavli (Shevuot 2b) asks explicitly:
מכדי תנא ממכות סליק מאי שנא דתני שבועות
The teacher just finished Makkot, why is he now teaching Shevuot? (my translation)
but a) that is probably a late addition to the text by the Savoraim, and b) it could just mean he finished the topic of "lashes" from the last chapter of Makkot, not that he finished a work with the title "Makkot".