just imho
first of all, does your tuner has input and output plus a stomp switch to on/off the tuner? If have, as follow
1) You can put it first in chain, since tuner is for the guitar, wont it be better when signal go straight to the tuner?
2) You can put it anywhere in the chain. Tune up. disengaged the tuner stompswitch. Engage the rest of the pedals and listen whether does it do any changes to your overall sound after the signal pass thru your tuner then to the rest of the pedals and lastly to amp. Reason for this method is, you helping yourself, to listen and hear which is the best position to have the tuner in the chain. Since we cant hear how the tone gonna be like, you have to help yourself. Plug in, plug out, do it over and over again to hear if theres any differences and finally stay with that position of tuner in the chain
And if you tuner only have a input. Iam afraid the only way is to tune up first then connect your guitar to the effect
Lastly, if your tuner has input/output jack plus the stomp switch to on/off, but you dont want the signal to pass thru the buffer which the tuner circuit might have. You can get a true bypass looper, connect the tuner in the send/return loop of the TB looper and the normal input/output the the rest of the chain of effect.
For true bypass looper, if having doubts, google it andread up on what it does. If you want to get it locally, i believe our forumite, brobluearkbro can make one for you at a reasonable price, another place to get is from
http://www.tymusiccenter.com or search for hub37 in the forum here.