Phase difference between two sinuisoidal signal
You can find phase between 2 sines, if you write it as a complex signal where 1st sine is a real part and second one is imaginary. But to do so it's necessary to rescale one component to fit another in its amplitude variation. Or another approach is to normalize both sines in amplitude value. There are some explanations:

We have signals $s_1(t)$ and $s_2(t)$, which are assumed to be sine waves. Before the measurement of their phase differences, we have to normalize there signals. The normalization process is:

$s^{norm}_i(t) = \frac {s_i(t)} {1.414 \cdot \mathrm{E}[\mid s_i \mid]}$

where $\mathrm{E}[\mid s \mid ]$ is mean value of module of $s(t)$. To perform normalization in real time it's necessary to track $\mathrm{E}[\mid s \mid ]$ constantly since the signal $s(t)$ can be non-stationary. Recurrent moving average filter is the case:

$s^{mean}_i(k) = a \cdot \mid s_i(k) \mid + (1-a) \cdot s^{mean}_i(k-1)$

where $a$ is inverse of integration time (or equivalently filter's length $K$) $a = \frac {1} {K}$ and $k$ sample index in discrete time representation.

Once we normalize both signals it is possible to estimate phase shift between them as

$s(t) = s^{norm}_1(t) + j \cdot s^{norm}_2(t)$

$\phi(t) = arg(s(t))$

$\phi(t) = tan^{-1}(\frac {\Im{s(t)}}{\Re{s(t)}})$

If it's real time implementation good practice is to use CORDIC to calculate the phase instead of $atan$ function.