In water, methanol is more acidic than water
The apparent contradiction comes from using a different standard state for water (activity of pure water defined as 1) and methanol (activity of approximately 1 mol/L defined as 1). So it is inappropriate to directly compare equilibrium constants or $\mathrm{p}K_\mathrm{a}$ values if in one system, a species is the solvent and in another one it is not.
Instead, consider the concentrations at a pH of 14 (e.g. roughly 1 mol/L $\ce{NaOH}$). At this pH, the ratio of water to hydroxide is 55:1, or roughly 2% dissociated. We can calculate the ratio of methanol to methoxide using the Henderson-Hasselbalch relationship (or straight from the equilibrium constant expression). It comes out to about 30:1, or roughly 3% dissociated. So methanol is the stronger acid because at a given pH, the ratio of deprotonated species to protonated species is higher. You could do the same at any other pH with the same conclusion that methanol is the stronger acid with water as the solvent.
Using $\mathrm{p}K_\mathrm{a}$ values for comparison
If you try to use the Henderson-Hasselbalch equation for water, you have to plug in "1" for the activity of water because that is what was used in the definition of the $\mathrm{p}K_\mathrm{a}$. If you do that, you find that the ratio of activities is 1:1, corresponding to 1 mol/L hydroxide and almost pure water, i.e. 55 mol/L. This is all internally consistent, but to compare it to methanol without comparing apples to oranges, it is appropriate to compare the degree of dissociation as done above.
In SCH's answer, the claim is made that in aqueous solution, "water is more dissociated than methanol". If you look at the degree of dissociation (mol fraction of undissociated vs dissociated) as I did above, this statement is incorrect. What is correct is that, using the more logical value of $\mathrm{p}K_\mathrm{a} = 14$ for water, the $\mathrm{p}K_\mathrm{a}$ of water is lower than that of methanol.
Solvent-dependence
[OP] ...we regard alkoxide ions as being more strongly basic than the hydroxide ion...
This statement was made in the context of organic chemistry. In this context, you will have solvents other than water. So you could compare methanol's and water's acidity in e.g. acetonitrile, DMSO or methanol or in solvent mixtures. This makes things complicated (see @Mithoron in the comments: "It depends"), and you would have to limit your question to a specific situation. The blanket statement that alkoxide ions are (always) more strongly basic than hydroxide ions is incorrect.