I analysed the mishnayot according to how they appear on Mechon Mamre and how they appear on Sefaria.
For Mechon Mamre's mishnayot, the raw data is here, where I removed punctuation and eliminated mishna numbering (and secondary numbering). The word count output is here. You can sort that list, find the corresponding line in the word count output, and compare that to the raw data. (Sorry this is cumbersome, there are better ways that take longer to implement.) The top 10 longest mishnayot by word count, according to Mechon Mamre, are:
- Eduyot 6:3 (319 words)
- Sota 8:1 (300 words)
- Yadayim 4:3 (290 words)
- Yevamot 14:4 (287 words)
- Middot 4:8 (244 words)
- Nazir 8:1 (236 words)
- Zevaḥim 6:9 (215 words)
- Sanhedrin 4:5 (212 words)
- Tamid 4:4 (206 words)
- Bechorot 8:1 (185 words)
For Sefaria's mishnayot, the raw data is here (pulled from here), and the word count output is here. The top 10 longest mishnayot by word count, according to Sefaria, are:
- Eduyot 6:3 (317 words)
- Sota 9:15 (297 words)
- Yadayim 4:3 (288 words)
- Kiddushin 14:4 (255 words)
- Tamid 4:3 (253 words)
- Sanhedrin 10:2 (239 words)
- Nazir 8:1 (236 words)
- Sanhedrin 4:5 (210 words)
- Zevaḥim 6:7 (209 words)
- Nedarim 3:11 (196 words)
All of this relates to collections of mishnayot. However, in the printed Talmud Bavli all of the mishnayot in the fourteenth perek of Masechet Zevachim are printed as one long continuous mishnah on dapim 112a-113a. So if you are learning gemara, that is the longest mishnah you will encounter. Similarly, the gemara at the end of Pesachim (98b) combines three mishnayot into one long mishnah of 273 words.