Metronomes and tuners are wonderful tools for helping to develop rhythmic and pitch precision. I think it is a good idea to use them occasionally, especially if you go for a long stretch of time without an in-person lesson from your teacher. Metronomes are especially valuable in working out the rhythms in slow passages of sankyoku pieces (the fast tegoto sections are actually easier), and tuners are useful for making sure that you are playing certain hard-to-tune notes high enough (such as go no hi) or low enough (such as tsu meri).
However, the goal is to internalize rhythmic facility and pitch discrimination, so it is important to work more often without these aids.
Through singing pieces while clapping, the rhythm enters your body, and you develop a neuro-muscular memory of particular rhythmic combinations. Rather than referencing the sound of an external mechanical beat, you are feeling the pulse as you make music. The traditional right-left clapping method used to teach the rhythms in Japanese music is a particularly effective tool.
Similarly with pitch: by listening very carefully as you play, adjusting your sound upwards and downwards until it feels exactly right, you develop an internal, body-centered pitch map. It is helpful to work with the exercises in the "pitch twin" tip on this page. For example, play a ro and check it against the tuner. Get the sound in your head. Sing it a few times. Now play a tsu dai meri and make sure it is exactly the same pitch as ro. Do the same thing with a second octave re and ichi san no u (ru), etc. etc. This develops your ear as well as your technique.
I have found that for many beginning students, pitch drifts downward -- you play flat on kari notes -- if you go too long without a lesson. If you are not taking lessons very regularly, I suggest occasionally using a tuner as a reference when you practice. And as for rhythm, always go back to singing pieces!