if you know, in advance, the frequency of the sinusoid, so only the phase (and perhaps the amplitude) is unknown, the simplest noise-immune method i know of to get amplitude and phase is (i'm gonna do this in continuous time and let you translate it to discrete time and eventually to MATLAB):
$$ x(t) = \sin(\omega t + \phi) + n(t) $$
compute
$$ \begin{align}
a & = \int\limits_0^{\frac{2 \pi}{\omega}} x(t) \sin(\omega t) dt \\
& = \int\limits_0^{\frac{2 \pi}{\omega}} \left(\sin(\omega t + \phi) + n(t) \right) \sin(\omega t) dt \\
& = \int\limits_0^{\frac{2 \pi}{\omega}} \sin(\omega t + \phi) \sin(\omega t) dt + \int\limits_0^{\frac{2 \pi}{\omega}} n(t) \sin(\omega t) dt \\
& = \frac{1}{2} \int\limits_0^{\frac{2 \pi}{\omega}} \cos(\phi) dt - \frac{1}{2} \int\limits_0^{\frac{2 \pi}{\omega}} \cos(2\omega t + \phi) dt + \int\limits_0^{\frac{2 \pi}{\omega}} n(t) \sin(\omega t) dt \\
& \approx \frac{1}{2} \int\limits_0^{\frac{2 \pi}{\omega}} \cos(\phi) dt \\
& = \frac{\pi}{\omega} \cos(\phi) \\
\end{align} $$
and
$$ \begin{align}
b & = \int\limits_0^{\frac{2 \pi}{\omega}} x(t) \cos(\omega t) dt \\
& = \int\limits_0^{\frac{2 \pi}{\omega}} \left(\sin(\omega t + \phi) + n(t) \right) \cos(\omega t) dt \\
& = \int\limits_0^{\frac{2 \pi}{\omega}} \sin(\omega t + \phi) \cos(\omega t) dt + \int\limits_0^{\frac{2 \pi}{\omega}} n(t) \cos(\omega t) dt \\
& = \frac{1}{2} \int\limits_0^{\frac{2 \pi}{\omega}} \sin(\phi) dt + \frac{1}{2} \int\limits_0^{\frac{2 \pi}{\omega}} \sin(2\omega t + \phi) dt + \int\limits_0^{\frac{2 \pi}{\omega}} n(t) \cos(\omega t) dt \\
& \approx \frac{1}{2} \int\limits_0^{\frac{2 \pi}{\omega}} \sin(\phi) dt \\
& = \frac{\pi}{\omega} \sin(\phi) \\
\end{align} $$
in both expressions (on the bottom line) we know the middle integral is zero and expect the integral on the right to tend toward zero because $n(t)$ is bipolar and ain't correlated with anything.
i think, then, that you'll find the phase $\phi$ to be:
$$ \phi = \arg\left\{a + jb \right\} $$
which is, if $a>0$
$$ \phi = \arctan\left(\frac{b}{a} \right) $$
otherwise, you might have to add or subtract $\pi$ to that expression.