You are correct. Estimating the instantaneous phase of a noisy sinusoid is NOT easy. I suggest you design a narrow bandpass filter such that your sinusoid-of-interest is in the filter's passband. (The better the filter the more noise that will be eliminated.) Pass your two signals through the bandpass filter to generate filtered signals $x_1[n]$ and $x_2[n]$. Next, pass your $x_1[n]$ and $x_2[n]$ signals through a Hilbert transformer to generate $\hat{x}_1[n]$ and $\hat{x}_2[n]$. Create two analytic (complex) signals as:
$$z_1[n] = x_1[n] + j \, \hat{x}_1[n],$$
and $$z_2[n] = x_2[n] + j \, \hat{x}_2[n]$$
where
$$ \begin{align}
\hat{x}[n] & = \mathcal{H}\{ x[n] \} \\
& = \sum\limits_{m=-\infty}^{+\infty} \frac{1 - (-1)^{m}}{\pi \, m} x[n-m] \\
\end{align} $$
Next, compute two instantaneous phase sequences:
$$\phi_1[n] = \arg\{z_1[n]\}$$
and $$\phi_2[n] = \arg\{z_2[n]\}.$$
Finally, compare the instantaneous phase difference between the $\phi_1[n]$ and $\phi_2[n]$ sequences.