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A modification of Dror's comment.

This probabilistic algorithm worked for me.

The main idea is to pick some $z$, compute $m=n - z^2$, factor $m$ with trial division and express it as a sum of two squares if possible. The probability of finding prime $m=4a+1$ or $2p$ is high enough for practical purposes.

The algorithm:

1. z:=0
2. z:=z+1
3. m:=n-z^2
4. if can't trial factor m goto 2
5. if m=x^2+y^2 (the factorization is known) then x^2+y^2+z^2=n. Done
6. goto 2

Here is a pari/gp program and example:

/*
? n=nextprime(10^220+30000)*nextprime(2^1000+40000000);n%8
%136 = 3
? t=threesquares(n);

? ##
  ***   last result computed in 2,210 ms.
? round(log(n))
%138 = 1200
*/

pl=10^6;\\ bound for trial division, may need change
default(primelimit,pl);
{
twosquares(n)=
local(K,i,v,p,c1,c2);
K=bnfinit(x^2+1);
v=bnfisintnorm(K,n);
for(i=1,#v,p=v[i];c1=polcoeff(p,0);c2=polcoeff(p,1);if(denominator(c1)==1&&denominator(c2)==1,return([c1,c2])) );
return([]);
}

{
threesquares(n)=
local(m,z,i,x1,y1,j,fa,g);
if(n/4^valuation(n,4)==7,return([]););
for(z=1,n,
\\forstep(z=sqrtint(n),1,-1,
m=n-z^2;
if(m%4==3,next);
print1(z," ",);
fa=factor(m,pl);
g=1;
for(i=1,#fa~,if(!ispseudoprime(fa[i,1])/*||!isprime(fa[i,1])*/||(fa[i,2]%2==1&&fa[i,1]%4==3),g=0;break; ));
if(!g,next);
print("\nfound ",z," "," m=",m,factor(m));
j=twosquares(m);
print("j=",j);
x1=abs(j[1]);
y1=abs(j[2]);
return([x1,y1,z]);
);
}