There are several other anionic ion pairing reagents.
Of the same family as TFA you can find longer perfluoro chain ion pairing reagents (i.e. heptafluorobutyric acid (HFBA) NFPA, TDFHA, PDFOA etc). You can also use alkyl sulfonic acids from hexa to dodecyl...
The longer the ion pairing reagent the longer the equilibration time so keep that in mind...
Here are a couple of publications that use different perfluorocarboxylic acids for the separation of underivatized amino acids and small peptides (but in theory they should work for any ionizable cationic analyte).
Ion-pair reversed-phase liquid chromatography for the determination of polar underivatized amino acids using pefluorinated carboxylic acids as ion pairing agent
K. Petritis, P. Chaimbault, C. Elfakir, M. Dreux
J. Chromatogr. A 833 (1999), 147-155.
Ion-pair reversed phase liquid chromatography electrospray mass spectrometry for the analysis of underivatized small peptides
K. Petritis, S. Brussaux, S. Guenu, C. Elfakir, M. Dreux
J. Chromatogr. A 957 (2002) 173-185