Why does my sinusoid look "AM" in shape?
This visual phenomenon appears because the maximum frequency is close to the Nyquist frequency, or half the sampling frequency. Sampling begins to approach the limit of $2$ samples per period, and thus the linear interpolation performed by Matlab becomes highly inaccurate. However, samples are correctly located, as you can see from the code where an higher sampling ('Oversampled') is superimposed:



Fs=200e6;
Ts=1/Fs;
NFFT=2^14;
Runtime=(NFFT-1)*Ts;
t=0:Ts:Runtime;
f_in=90*1e6;
y_in=sin(2*pi *f_in *t);

Fs2=20*Fs;
Ts2=1/Fs2;
NFFT=2^14;
t2=0:Ts2:Runtime;
f_in=90*1e6;
y_in2=sin(2*pi *f_in *t2);

clf;hold on;
plot(t,y_in,'x')
plot(t2,y_in2,'-')
ylim([-1.5 1.5])
xlim([5.2 5.4]*1e-6)
legend('Original','Oversampled')