You can use text.
text(x, y, s, fontsize=12)
text coordinates can be given relative to the axis, so the position of your text will be independent of the size of the plot:
The default transform specifies that text is in data coords, alternatively, you can specify text in axis coords (0,0 is lower-left and 1,1 is upper-right). The example below places text in the center of the axes::
text(0.5, 0.5,'matplotlib',
horizontalalignment='center',
verticalalignment='center',
transform = ax.transAxes)
To prevent the text to interfere with any point of your scatter is more difficult afaik. The easier method is to set y_axis (ymax in ylim((ymin,ymax))) to a value a bit higher than the max y-coordinate of your points. In this way you will always have this free space for the text.
EDIT: here you have an example:
In [17]: from pylab import figure, text, scatter, show
In [18]: f = figure()
In [19]: ax = f.add_subplot(111)
In [20]: scatter([3,5,2,6,8],[5,3,2,1,5])
Out[20]: <matplotlib.collections.CircleCollection object at 0x0000000007439A90>
In [21]: text(0.1, 0.9,'matplotlib', ha='center', va='center', transform=ax.transAxes)
Out[21]: <matplotlib.text.Text object at 0x0000000007415B38>
In [22]:
The ha and va parameters set the alignment of your text relative to the insertion point. ie. ha='left' is a good set to prevent a long text to go out of the left axis when the frame is reduced (made narrower) manually.