The efficient way to do this with numpy is to reshape your index array to match the axes they are indexing i.e.
In [103]: a=numpy.arange(100).reshape(10,10)
In [104]: a
Out[104]:
array([[ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9],
[10, 11, 12, 13, 14, 15, 16, 17, 18, 19],
[20, 21, 22, 23, 24, 25, 26, 27, 28, 29],
[30, 31, 32, 33, 34, 35, 36, 37, 38, 39],
[40, 41, 42, 43, 44, 45, 46, 47, 48, 49],
[50, 51, 52, 53, 54, 55, 56, 57, 58, 59],
[60, 61, 62, 63, 64, 65, 66, 67, 68, 69],
[70, 71, 72, 73, 74, 75, 76, 77, 78, 79],
[80, 81, 82, 83, 84, 85, 86, 87, 88, 89],
[90, 91, 92, 93, 94, 95, 96, 97, 98, 99]])
In [105]: x=numpy.array([3,6,9])
In [106]: y=numpy.array([2,7,8])
In [107]: a[x[:,numpy.newaxis],y[numpy.newaxis,:]]
Out[107]:
array([[32, 37, 38],
[62, 67, 68],
[92, 97, 98]])
Numpy's rules of broadcasting are your friend (and so much better than matlab)...
HTH