You raise a good point.
I know a few micro budget indies use eg a H4n with Rode NTG3 and output the H4n into their DSLR (eg Canon 5D Mk3) so the 'baseline' audio captured by the camera is better (than that offered by the camera's 'mic' and internals). Why? So post audio syncing may be a bit easier and less manual syncing/intervention is required.
I considered this when I was purchasing my gear... But prior to buying Pluraleyes, I asked the support team at Red Giant whether my Canon 6D's 'mic' and internals would be able to capture an audio signal good enough for Pluraleyes to sync to, or should I do eg the above (I'm using a Tascam DR40 and Audio Technica AT4053b with Canon 6D). They said the Canon's signal should be good enough for most scenes - so maybe not all.
To the OP, if you want to do this, you'd need something like below (-25dB Attenuation cable). The signal from the H4n would be far too hot for your camera. It needs to be brought in line with what your camera can handle. Also turn the sound capture level of your DSLR down to the lowest possible level then raise it one - so it's just one click above the minimum level. You don't want your camera's preamps (which are very sub-par quality) ruining the audio - you want to use the H4n's (which are a good bit better - but not great).
Whirlwind WHH4NL 3.5 MON Line-to-Microphone Attenuator Cable for HDSLR Cameras
http://www.bhphotovideo.com/c/produ...NL3_5MON_WHH4NL3_5MON_Line_to_Microphone.html
Note if you're not using a quality external mic, I would not do this. If you're using the mics on the H4n save the $35. You can sync on the audio captured directly by the camera.
If Pluraleyes cannot sync a particular scene, provided you clapper-boarded it, you should still be able to manually sync it.